Input: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/inputs/xbf Working: n-1-18.cluster.ucsf.bkslab.org:/scratch/xiaobo/129831/xbf-8058088.32 Result: /scratch/xiaobo/129831/xbf-8058088.32 Output: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbf Task: /mnt/nfs/soft/dock/versions/dock37/DOCK-3.7.4rc1/ligand/generate/build_database_ligand.sh --no-db --no-solv --no-mol2 --single --covalent --pre-tautomerized --permissive-taut-prot /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/inputs/xbf mkdir: created directory `/scratch/xiaobo/129831' mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32' /scratch/xiaobo/129831/xbf-8058088.32 /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/logs NOTICE: Using permissive tautomer and protomer thresholds. Could produce many protomers! STORE_PROTOMERS is not set! Will keep all results to finished directory mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working' mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/protonate' Storing results in /scratch/xiaobo/129831/xbf-8058088.32/finished Working in /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 /scratch/xiaobo/129831/xbf-8058088.32/working/protonate /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Using inputs as protomers/tautomers. No processing done 478 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/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Bulk generating 3D conformations all protomers in /scratch/xiaobo/129831/xbf-8058088.32/working/3D mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/3D' We are using corina for 3D embeding debuging info:: /scratch/xiaobo/129831/xbf-8058088.32/working/protonate/xbf-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 ZINC001180968174 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building' mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180968174' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180968174 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for ZINC001180968174 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180968174/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180968174 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/1 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(c2cc(=O)c3ccccc3o2)c1NC(=O)[C@]([O-])([SiH3])CCc1ccccc1) `ZINC001180968174.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001180968174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180968174/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001180968174 none COc1cccc(c2cc(=O)c3ccccc3o2)c1NC(=O)[C@]([O-])([SiH3])CCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 1, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 15, 15, 15, 7, 15, 15, 15, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 3, 3, 1, 3, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 20, 20, 20, 15, 15, 15, 43, 43, 43, 43, 43, 3, 6, 6, 6, 6, 7, 7, 7, 7, 7] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180968174 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001180968174 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/finished' Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180968174/0.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180968174 Building ZINC001180968232 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180968232' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180968232 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001180968232 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180968232/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180968232 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 2) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/2 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/2' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1ccc(C2CCN(C(=O)[C@@]([O-])([SiH3])CCc3ccccc3)CC2)cc1) `ZINC001180968232.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001180968232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180968232/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001180968232 none CC(C)(C)OC(=O)Nc1ccc(C2CCN(C(=O)[C@@]([O-])([SiH3])CCc3ccccc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 26, 6, 4, 6, 6, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 5, 5, 6, 6, 5, 6, 6, 2, 2, 6, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 18, 6, 6, 2, 2, 2, 2, 2, 5, 5, 5, 5, 6, 6, 6, 6, 6, 2, 2, 2, 2, 6, 6] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 107 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180968232 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180968232/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180968232 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 3) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/3 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/3' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1ccc(C2CCN(C(=O)[C@]([O-])([SiH3])CCc3ccccc3)CC2)cc1) `ZINC001180968232.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001180968232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180968232/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001180968232 none CC(C)(C)OC(=O)Nc1ccc(C2CCN(C(=O)[C@]([O-])([SiH3])CCc3ccccc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 29, 21, 29, 8, 5, 8, 8, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 5, 5, 7, 7, 6, 7, 7, 3, 3, 8, 8, 29, 29, 29, 29, 29, 29, 29, 29, 29, 21, 8, 8, 3, 3, 3, 3, 3, 5, 5, 5, 5, 7, 7, 7, 7, 7, 3, 3, 3, 3, 8, 8] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 122 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180968232 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001180968232 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180968232/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180968232/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180968232 Building ZINC001180968232 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180968232' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180968232 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001180968232 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180968232/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180968232 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 2) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/2: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1ccc(C2CCN(C(=O)[C@@]([O-])([SiH3])CCc3ccccc3)CC2)cc1) `ZINC001180968232.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001180968232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180968232/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001180968232 none CC(C)(C)OC(=O)Nc1ccc(C2CCN(C(=O)[C@@]([O-])([SiH3])CCc3ccccc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 26, 6, 4, 6, 6, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 5, 5, 6, 6, 5, 6, 6, 2, 2, 6, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 18, 6, 6, 2, 2, 2, 2, 2, 5, 5, 5, 5, 6, 6, 6, 6, 6, 2, 2, 2, 2, 6, 6] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 107 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180968232 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180968232/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180968232 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 3) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/3: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1ccc(C2CCN(C(=O)[C@]([O-])([SiH3])CCc3ccccc3)CC2)cc1) `ZINC001180968232.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001180968232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180968232/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001180968232 none CC(C)(C)OC(=O)Nc1ccc(C2CCN(C(=O)[C@]([O-])([SiH3])CCc3ccccc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 29, 21, 29, 8, 5, 8, 8, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 5, 5, 7, 7, 6, 7, 7, 3, 3, 8, 8, 29, 29, 29, 29, 29, 29, 29, 29, 29, 21, 8, 8, 3, 3, 3, 3, 3, 5, 5, 5, 5, 7, 7, 7, 7, 7, 3, 3, 3, 3, 8, 8] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 122 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180968232 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001180968232 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180968232/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180968232/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180968232 Building ZINC001180969869 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180969869' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180969869 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001180969869 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180969869/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180969869 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 4) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/4 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/4' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1coc(c2ccc(OCc3ccccc3)cc2)n1)[C@]([O-])([SiH3])CCc1ccccc1) `ZINC001180969869.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001180969869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180969869/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001180969869 none O=C(NCc1coc(c2ccc(OCc3ccccc3)cc2)n1)[C@]([O-])([SiH3])CCc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.3', 'O.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: [11, 1, 8, 5, 1, 1, 12, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 19, 19, 19, 19, 35, 35, 29, 29, 50, 50, 50, 50, 50, 50, 50, 35, 35, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 19, 35, 35, 50, 50, 50, 50, 50, 50, 50, 35, 35, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 1, 56, 55, 48, 49, 50, 51, 52, 53, 54, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180969869 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180969869/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180969869 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 5) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/5 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/5' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1coc(c2ccc(OCc3ccccc3)cc2)n1)[C@@]([O-])([SiH3])CCc1ccccc1) `ZINC001180969869.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001180969869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180969869/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001180969869 none O=C(NCc1coc(c2ccc(OCc3ccccc3)cc2)n1)[C@@]([O-])([SiH3])CCc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.3', 'O.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: [11, 1, 8, 5, 1, 1, 12, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 19, 19, 19, 19, 35, 35, 29, 29, 50, 50, 50, 50, 50, 50, 50, 35, 35, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 19, 35, 35, 50, 50, 50, 50, 50, 50, 50, 35, 35, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 1, 56, 55, 48, 49, 50, 51, 52, 53, 54, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180969869 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001180969869 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180969869/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180969869/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180969869 Building ZINC001180969869 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180969869' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180969869 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001180969869 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180969869/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180969869 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 4) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/4: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1coc(c2ccc(OCc3ccccc3)cc2)n1)[C@]([O-])([SiH3])CCc1ccccc1) `ZINC001180969869.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001180969869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180969869/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001180969869 none O=C(NCc1coc(c2ccc(OCc3ccccc3)cc2)n1)[C@]([O-])([SiH3])CCc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.3', 'O.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: [11, 1, 8, 5, 1, 1, 12, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 19, 19, 19, 19, 35, 35, 29, 29, 50, 50, 50, 50, 50, 50, 50, 35, 35, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 19, 35, 35, 50, 50, 50, 50, 50, 50, 50, 35, 35, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 1, 56, 55, 48, 49, 50, 51, 52, 53, 54, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180969869 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180969869/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180969869 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 5) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/5: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1coc(c2ccc(OCc3ccccc3)cc2)n1)[C@@]([O-])([SiH3])CCc1ccccc1) `ZINC001180969869.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001180969869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180969869/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001180969869 none O=C(NCc1coc(c2ccc(OCc3ccccc3)cc2)n1)[C@@]([O-])([SiH3])CCc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.3', 'O.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: [11, 1, 8, 5, 1, 1, 12, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 19, 19, 19, 19, 35, 35, 29, 29, 50, 50, 50, 50, 50, 50, 50, 35, 35, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 19, 35, 35, 50, 50, 50, 50, 50, 50, 50, 35, 35, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 1, 56, 55, 48, 49, 50, 51, 52, 53, 54, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180969869 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001180969869 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180969869/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180969869/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180969869 Building ZINC001180989075 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180989075' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180989075 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001180989075 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180989075/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180989075 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 6) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/6 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/6' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001180989075.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001180989075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180989075/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001180989075 none CC(C)(C)OC(=O)N1CCC[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 37, 50, 37, 37, 37, 37, 22, 37, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37, 15, 15, 10, 10, 2, 2, 1, 2, 37, 37, 37, 37] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180989075 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180989075/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180989075 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 7) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/7 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/7' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@@H](CCNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001180989075.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001180989075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180989075/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001180989075 none CC(C)(C)OC(=O)N1CCC[C@@H](CCNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 50, 40, 40, 40, 40, 22, 40, 12, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 40, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 40, 40, 40, 40, 40, 40, 17, 17, 12, 12, 2, 2, 1, 2, 40, 40, 40, 40] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180989075 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001180989075 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180989075/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180989075/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180989075 Building ZINC001180989075 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180989075' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180989075 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001180989075 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180989075/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180989075 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 6) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/6: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001180989075.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001180989075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180989075/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001180989075 none CC(C)(C)OC(=O)N1CCC[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 37, 50, 37, 37, 37, 37, 22, 37, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37, 15, 15, 10, 10, 2, 2, 1, 2, 37, 37, 37, 37] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180989075 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180989075/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180989075 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 7) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/7: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@@H](CCNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001180989075.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001180989075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180989075/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001180989075 none CC(C)(C)OC(=O)N1CCC[C@@H](CCNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 50, 40, 40, 40, 40, 22, 40, 12, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 40, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 40, 40, 40, 40, 40, 40, 17, 17, 12, 12, 2, 2, 1, 2, 40, 40, 40, 40] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180989075 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001180989075 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180989075/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180989075/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180989075 Building ZINC001180989076 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180989076' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180989076 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001180989076 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180989076/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180989076 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 8) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/8 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/8' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@H](CCNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001180989076.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001180989076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180989076/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001180989076 none CC(C)(C)OC(=O)N1CCC[C@H](CCNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 34, 50, 34, 34, 34, 34, 21, 34, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 34, 34, 34, 34, 34, 12, 12, 10, 10, 2, 2, 1, 2, 34, 34, 34, 34] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180989076 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180989076/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180989076 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 9) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/9 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/9' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@H](CCNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001180989076.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001180989076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180989076/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001180989076 none CC(C)(C)OC(=O)N1CCC[C@H](CCNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 36, 50, 36, 36, 36, 36, 23, 36, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 36, 36, 13, 13, 9, 9, 2, 2, 2, 2, 36, 36, 36, 36] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180989076 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001180989076 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180989076/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180989076/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180989076 Building ZINC001180989076 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180989076' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180989076 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001180989076 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180989076/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180989076 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 8) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/8: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@H](CCNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001180989076.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001180989076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180989076/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001180989076 none CC(C)(C)OC(=O)N1CCC[C@H](CCNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 34, 50, 34, 34, 34, 34, 21, 34, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 34, 34, 34, 34, 34, 12, 12, 10, 10, 2, 2, 1, 2, 34, 34, 34, 34] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180989076 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180989076/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180989076 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 9) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/9: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@H](CCNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001180989076.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001180989076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180989076/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001180989076 none CC(C)(C)OC(=O)N1CCC[C@H](CCNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 36, 50, 36, 36, 36, 36, 23, 36, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 36, 36, 13, 13, 9, 9, 2, 2, 2, 2, 36, 36, 36, 36] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180989076 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001180989076 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180989076/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180989076/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001180989076 Building ZINC001181375041 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181375041' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181375041 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001181375041 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181375041/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181375041 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 10) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/10 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/10' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ncnc2[nH]nc(c3ccc(Oc4ccccc4)cc3)c21)[C@]([O-])([SiH3])Cc1ccccc1) `ZINC001181375041.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001181375041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181375041/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001181375041 none O=C(Nc1ncnc2[nH]nc(c3ccc(Oc4ccccc4)cc3)c21)[C@]([O-])([SiH3])Cc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 8, 1, 8, 6, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 6, 8, 43, 48, 48, 43, 48, 48, 8, 8, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 2, 4, 8, 8, 48, 48, 43, 48, 48, 8, 8, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [1, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181375041 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181375041/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181375041 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 11) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/11 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/11' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ncnc2[nH]nc(c3ccc(Oc4ccccc4)cc3)c21)[C@@]([O-])([SiH3])Cc1ccccc1) `ZINC001181375041.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001181375041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181375041/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001181375041 none O=C(Nc1ncnc2[nH]nc(c3ccc(Oc4ccccc4)cc3)c21)[C@@]([O-])([SiH3])Cc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 8, 1, 8, 6, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 4, 6, 42, 48, 48, 42, 48, 48, 8, 8, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 2, 4, 8, 8, 48, 48, 42, 48, 48, 8, 8, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [1, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181375041 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001181375041 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181375041/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181375041/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181375041 Building ZINC001181375041 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181375041' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181375041 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001181375041 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181375041/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181375041 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 10) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/10: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ncnc2[nH]nc(c3ccc(Oc4ccccc4)cc3)c21)[C@]([O-])([SiH3])Cc1ccccc1) `ZINC001181375041.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001181375041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181375041/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001181375041 none O=C(Nc1ncnc2[nH]nc(c3ccc(Oc4ccccc4)cc3)c21)[C@]([O-])([SiH3])Cc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 8, 1, 8, 6, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 6, 8, 43, 48, 48, 43, 48, 48, 8, 8, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 2, 4, 8, 8, 48, 48, 43, 48, 48, 8, 8, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [1, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181375041 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181375041/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181375041 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 11) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/11: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ncnc2[nH]nc(c3ccc(Oc4ccccc4)cc3)c21)[C@@]([O-])([SiH3])Cc1ccccc1) `ZINC001181375041.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001181375041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181375041/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001181375041 none O=C(Nc1ncnc2[nH]nc(c3ccc(Oc4ccccc4)cc3)c21)[C@@]([O-])([SiH3])Cc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 8, 1, 8, 6, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 4, 6, 42, 48, 48, 42, 48, 48, 8, 8, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 2, 4, 8, 8, 48, 48, 42, 48, 48, 8, 8, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [1, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181375041 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001181375041 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181375041/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181375041/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181375041 Building ZINC001181376387 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181376387' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181376387 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001181376387 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181376387/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181376387 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 12) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/12 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/12' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(O[C@H](c2ccc(Cl)cc2)c2ccccn2)CC1)[C@]([O-])([SiH3])Cc1ccccc1) `ZINC001181376387.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001181376387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181376387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001181376387 none O=C(N1CCC(O[C@H](c2ccc(Cl)cc2)c2ccccn2)CC1)[C@]([O-])([SiH3])Cc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 5, 7, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 4, 4, 4, 4, 16, 38, 38, 39, 39, 38, 38, 39, 39, 38, 43, 43, 43, 43, 43, 4, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 39, 39, 39, 39, 43, 43, 43, 43, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [24, 1, 26, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181376387 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181376387/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181376387 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 13) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/13 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/13' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(O[C@H](c2ccc(Cl)cc2)c2ccccn2)CC1)[C@@]([O-])([SiH3])Cc1ccccc1) `ZINC001181376387.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001181376387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181376387/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001181376387 none O=C(N1CCC(O[C@H](c2ccc(Cl)cc2)c2ccccn2)CC1)[C@@]([O-])([SiH3])Cc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 5, 7, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 4, 4, 4, 4, 17, 42, 42, 42, 42, 42, 42, 42, 42, 42, 44, 44, 44, 44, 44, 4, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 42, 42, 42, 42, 44, 44, 44, 44, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [24, 1, 26, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 156 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181376387 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001181376387 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181376387/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181376387/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181376387 Building ZINC001181376387 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181376387' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181376387 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001181376387 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181376387/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181376387 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 12) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/12: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(O[C@H](c2ccc(Cl)cc2)c2ccccn2)CC1)[C@]([O-])([SiH3])Cc1ccccc1) `ZINC001181376387.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001181376387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181376387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001181376387 none O=C(N1CCC(O[C@H](c2ccc(Cl)cc2)c2ccccn2)CC1)[C@]([O-])([SiH3])Cc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 5, 7, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 4, 4, 4, 4, 16, 38, 38, 39, 39, 38, 38, 39, 39, 38, 43, 43, 43, 43, 43, 4, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 39, 39, 39, 39, 43, 43, 43, 43, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [24, 1, 26, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181376387 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181376387/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181376387 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 13) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/13: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(O[C@H](c2ccc(Cl)cc2)c2ccccn2)CC1)[C@@]([O-])([SiH3])Cc1ccccc1) `ZINC001181376387.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001181376387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181376387/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001181376387 none O=C(N1CCC(O[C@H](c2ccc(Cl)cc2)c2ccccn2)CC1)[C@@]([O-])([SiH3])Cc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 5, 7, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 4, 4, 4, 4, 17, 42, 42, 42, 42, 42, 42, 42, 42, 42, 44, 44, 44, 44, 44, 4, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 42, 42, 42, 42, 44, 44, 44, 44, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [24, 1, 26, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 156 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181376387 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001181376387 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181376387/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181376387/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181376387 Building ZINC001181376391 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181376391' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181376391 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001181376391 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181376391/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181376391 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 14) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/14 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/14' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(O[C@@H](c2ccc(Cl)cc2)c2ccccn2)CC1)[C@]([O-])([SiH3])Cc1ccccc1) `ZINC001181376391.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001181376391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181376391/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001181376391 none O=C(N1CCC(O[C@@H](c2ccc(Cl)cc2)c2ccccn2)CC1)[C@]([O-])([SiH3])Cc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 5, 7, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 4, 4, 4, 4, 17, 40, 40, 41, 41, 40, 40, 41, 41, 40, 44, 44, 44, 44, 44, 4, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 41, 41, 41, 41, 44, 44, 44, 44, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [24, 1, 26, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 159 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181376391 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181376391/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181376391 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 15) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/15 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/15' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(O[C@@H](c2ccc(Cl)cc2)c2ccccn2)CC1)[C@@]([O-])([SiH3])Cc1ccccc1) `ZINC001181376391.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001181376391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181376391/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001181376391 none O=C(N1CCC(O[C@@H](c2ccc(Cl)cc2)c2ccccn2)CC1)[C@@]([O-])([SiH3])Cc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 5, 7, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 4, 4, 4, 4, 17, 37, 37, 37, 37, 37, 37, 37, 37, 37, 38, 38, 38, 38, 38, 4, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 37, 37, 37, 37, 38, 38, 38, 38, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [24, 1, 26, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 133 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181376391 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001181376391 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181376391/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181376391/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181376391 Building ZINC001181376391 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181376391' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181376391 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001181376391 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181376391/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181376391 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 14) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/14: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(O[C@@H](c2ccc(Cl)cc2)c2ccccn2)CC1)[C@]([O-])([SiH3])Cc1ccccc1) `ZINC001181376391.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001181376391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181376391/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001181376391 none O=C(N1CCC(O[C@@H](c2ccc(Cl)cc2)c2ccccn2)CC1)[C@]([O-])([SiH3])Cc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 5, 7, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 4, 4, 4, 4, 17, 40, 40, 41, 41, 40, 40, 41, 41, 40, 44, 44, 44, 44, 44, 4, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 41, 41, 41, 41, 44, 44, 44, 44, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [24, 1, 26, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 159 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181376391 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181376391/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181376391 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 15) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/15: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(O[C@@H](c2ccc(Cl)cc2)c2ccccn2)CC1)[C@@]([O-])([SiH3])Cc1ccccc1) `ZINC001181376391.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001181376391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181376391/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001181376391 none O=C(N1CCC(O[C@@H](c2ccc(Cl)cc2)c2ccccn2)CC1)[C@@]([O-])([SiH3])Cc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 5, 7, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 4, 4, 4, 4, 17, 37, 37, 37, 37, 37, 37, 37, 37, 37, 38, 38, 38, 38, 38, 4, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 37, 37, 37, 37, 38, 38, 38, 38, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [24, 1, 26, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 133 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181376391 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001181376391 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181376391/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181376391/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181376391 Building ZINC001181377411 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181377411' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181377411 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001181377411 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181377411/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181377411 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 16) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/16 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/16' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc2nccc(Oc3ccc(NC(=O)[C@@]([O-])([SiH3])Cc4ccccc4)cc3)c2cc1OC) `ZINC001181377411.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001181377411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181377411/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001181377411 none COc1cc2nccc(Oc3ccc(NC(=O)[C@@]([O-])([SiH3])Cc4ccccc4)cc3)c2cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 1, 1, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 31, 31, 31, 31, 31, 31, 31, 19, 2, 2, 11, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 11, 11, 31, 31, 31, 31, 50, 50, 50, 50, 31, 31, 31, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11, 31, 50, 50, 50] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181377411 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181377411/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181377411 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 17) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/17 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/17' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc2nccc(Oc3ccc(NC(=O)[C@]([O-])([SiH3])Cc4ccccc4)cc3)c2cc1OC) `ZINC001181377411.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001181377411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181377411/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001181377411 none COc1cc2nccc(Oc3ccc(NC(=O)[C@]([O-])([SiH3])Cc4ccccc4)cc3)c2cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 1, 1, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 30, 30, 30, 30, 30, 30, 30, 23, 7, 3, 11, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 11, 11, 30, 30, 30, 30, 50, 50, 50, 50, 30, 30, 30, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11, 30, 50, 50, 50] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181377411 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001181377411 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181377411/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181377411/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181377411 Building ZINC001181377411 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181377411' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181377411 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001181377411 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181377411/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181377411 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 16) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/16: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc2nccc(Oc3ccc(NC(=O)[C@@]([O-])([SiH3])Cc4ccccc4)cc3)c2cc1OC) `ZINC001181377411.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001181377411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181377411/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001181377411 none COc1cc2nccc(Oc3ccc(NC(=O)[C@@]([O-])([SiH3])Cc4ccccc4)cc3)c2cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 1, 1, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 31, 31, 31, 31, 31, 31, 31, 19, 2, 2, 11, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 11, 11, 31, 31, 31, 31, 50, 50, 50, 50, 31, 31, 31, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11, 31, 50, 50, 50] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181377411 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181377411/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181377411 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 17) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/17: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc2nccc(Oc3ccc(NC(=O)[C@]([O-])([SiH3])Cc4ccccc4)cc3)c2cc1OC) `ZINC001181377411.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001181377411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181377411/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001181377411 none COc1cc2nccc(Oc3ccc(NC(=O)[C@]([O-])([SiH3])Cc4ccccc4)cc3)c2cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 1, 1, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 30, 30, 30, 30, 30, 30, 30, 23, 7, 3, 11, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 11, 11, 30, 30, 30, 30, 50, 50, 50, 50, 30, 30, 30, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11, 30, 50, 50, 50] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181377411 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001181377411 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181377411/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181377411/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181377411 Building ZINC001181377697 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181377697' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181377697 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001181377697 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181377697/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181377697 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 18) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/18 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/18' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C(=O)Nc2cccc(Cl)c2C)cc1NC(=O)[C@@]([O-])([SiH3])Cc1ccccc1) `ZINC001181377697.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001181377697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181377697/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001181377697 none COc1ccc(C(=O)Nc2cccc(Cl)c2C)cc1NC(=O)[C@@]([O-])([SiH3])Cc1ccccc1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 16, 1, 5, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 6, 6, 6, 6, 6, 10, 10, 10, 31, 31, 27, 31, 31, 31, 31, 6, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 9, 9, 9, 6, 6, 10, 31, 31, 31, 31, 31, 31, 6, 3, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181377697 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181377697/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181377697 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 19) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/19 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/19' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C(=O)Nc2cccc(Cl)c2C)cc1NC(=O)[C@]([O-])([SiH3])Cc1ccccc1) `ZINC001181377697.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001181377697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181377697/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001181377697 none COc1ccc(C(=O)Nc2cccc(Cl)c2C)cc1NC(=O)[C@]([O-])([SiH3])Cc1ccccc1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 16, 1, 5, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 6, 6, 6, 6, 6, 10, 10, 10, 31, 31, 31, 31, 31, 31, 31, 6, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 9, 9, 9, 6, 6, 10, 31, 31, 31, 31, 31, 31, 6, 3, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181377697 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001181377697 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181377697/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181377697/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181377697 Building ZINC001181377697 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181377697' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181377697 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001181377697 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181377697/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181377697 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 18) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/18: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C(=O)Nc2cccc(Cl)c2C)cc1NC(=O)[C@@]([O-])([SiH3])Cc1ccccc1) `ZINC001181377697.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001181377697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181377697/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001181377697 none COc1ccc(C(=O)Nc2cccc(Cl)c2C)cc1NC(=O)[C@@]([O-])([SiH3])Cc1ccccc1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 16, 1, 5, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 6, 6, 6, 6, 6, 10, 10, 10, 31, 31, 27, 31, 31, 31, 31, 6, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 9, 9, 9, 6, 6, 10, 31, 31, 31, 31, 31, 31, 6, 3, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181377697 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181377697/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181377697 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 19) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/19: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C(=O)Nc2cccc(Cl)c2C)cc1NC(=O)[C@]([O-])([SiH3])Cc1ccccc1) `ZINC001181377697.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001181377697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181377697/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001181377697 none COc1ccc(C(=O)Nc2cccc(Cl)c2C)cc1NC(=O)[C@]([O-])([SiH3])Cc1ccccc1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 16, 1, 5, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 6, 6, 6, 6, 6, 10, 10, 10, 31, 31, 31, 31, 31, 31, 31, 6, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 9, 9, 9, 6, 6, 10, 31, 31, 31, 31, 31, 31, 6, 3, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181377697 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001181377697 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181377697/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181377697/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181377697 Building ZINC001181867219 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181867219' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181867219 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001181867219 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181867219/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181867219 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 20) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/20 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/20' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1ccc2c(c1)CCCN2C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001181867219.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001181867219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181867219/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001181867219 none CC(C)(C)OC(=O)Nc1ccc2c(c1)CCCN2C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 28, 20, 28, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 38, 38, 38, 38, 38, 38, 38, 38, 38, 20, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181867219 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181867219/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181867219 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 21) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/21 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/21' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1ccc2c(c1)CCCN2C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001181867219.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001181867219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181867219/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001181867219 none CC(C)(C)OC(=O)Nc1ccc2c(c1)CCCN2C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 37, 38, 38, 29, 21, 29, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 38, 38, 38, 38, 38, 38, 38, 38, 38, 21, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181867219 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001181867219 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181867219/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181867219/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181867219 Building ZINC001181867219 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181867219' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181867219 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001181867219 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181867219/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181867219 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 20) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/20: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1ccc2c(c1)CCCN2C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001181867219.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001181867219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181867219/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001181867219 none CC(C)(C)OC(=O)Nc1ccc2c(c1)CCCN2C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 28, 20, 28, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 38, 38, 38, 38, 38, 38, 38, 38, 38, 20, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181867219 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181867219/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181867219 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 21) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/21: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1ccc2c(c1)CCCN2C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001181867219.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001181867219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181867219/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001181867219 none CC(C)(C)OC(=O)Nc1ccc2c(c1)CCCN2C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 37, 38, 38, 29, 21, 29, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 38, 38, 38, 38, 38, 38, 38, 38, 38, 21, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181867219 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001181867219 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181867219/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181867219/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001181867219 Building ZINC001182229331 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182229331' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182229331 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182229331 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182229331/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182229331 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 22) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/22 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/22' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccccc2c2ccc(CN(C)C)cc2)cc1Cl) `ZINC001182229331.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182229331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182229331/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001182229331 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccccc2c2ccc(CN(C)C)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 1, 1, 1, 1, 16, 7, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 29, 29, 29, 15, 15, 4, 4, 4, 8, 8, 8, 4, 4, 2, 9, 9, 15, 15, 15, 15, 15, 15, 29, 29, 29, 29, 29, 29, 29, 29, 15, 15, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182229331 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182229331/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182229331 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 23) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/23 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/23' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2c2ccc(CN(C)C)cc2)cc1Cl) `ZINC001182229331.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182229331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182229331/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001182229331 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2c2ccc(CN(C)C)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 1, 1, 1, 1, 16, 7, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 29, 29, 29, 15, 15, 4, 4, 4, 8, 8, 8, 4, 4, 2, 9, 9, 15, 15, 15, 15, 15, 15, 29, 29, 29, 29, 29, 29, 29, 29, 15, 15, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182229331 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001182229331 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182229331/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182229331/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182229331 Building ZINC001182229331 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182229331' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182229331 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182229331 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182229331/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182229331 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 22) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/22: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccccc2c2ccc(CN(C)C)cc2)cc1Cl) `ZINC001182229331.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182229331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182229331/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001182229331 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccccc2c2ccc(CN(C)C)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 1, 1, 1, 1, 16, 7, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 29, 29, 29, 15, 15, 4, 4, 4, 8, 8, 8, 4, 4, 2, 9, 9, 15, 15, 15, 15, 15, 15, 29, 29, 29, 29, 29, 29, 29, 29, 15, 15, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182229331 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182229331/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182229331 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 23) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/23: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2c2ccc(CN(C)C)cc2)cc1Cl) `ZINC001182229331.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182229331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182229331/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001182229331 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2c2ccc(CN(C)C)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 1, 1, 1, 1, 16, 7, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 29, 29, 29, 15, 15, 4, 4, 4, 8, 8, 8, 4, 4, 2, 9, 9, 15, 15, 15, 15, 15, 15, 29, 29, 29, 29, 29, 29, 29, 29, 15, 15, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182229331 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001182229331 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182229331/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182229331/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182229331 Building ZINC001182382107 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001182382107 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 24) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/24 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/24' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1) `ZINC001182382107.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182382107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001182382107 none CC(C)c1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 33, 32, 33, 33, 24, 15, 24, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 28, 47, 47, 47, 47, 47, 47, 47, 47, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 15, 15, 3, 3, 3, 1, 3, 3, 47, 47, 47, 47, 47, 47, 47, 47, 33, 33] 50 rigid atoms, others: [11, 13, 15, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 166 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 25) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/25 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/25' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1) `ZINC001182382107.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182382107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001182382107 none CC(C)c1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 35, 30, 17, 30, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 34, 49, 49, 49, 49, 49, 49, 49, 49, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 17, 17, 4, 3, 3, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 35, 35] 50 rigid atoms, others: [11, 13, 15, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 164 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 26) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/26 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/26' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1) `ZINC001182382107.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001182382107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001182382107 none CC(C)c1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 33, 32, 33, 33, 24, 15, 24, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 28, 47, 47, 47, 47, 47, 47, 47, 47, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 15, 15, 3, 3, 3, 1, 3, 3, 47, 47, 47, 47, 47, 47, 47, 47, 33, 33] 50 rigid atoms, others: [11, 13, 15, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 166 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 27) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/27 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/27' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1) `ZINC001182382107.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001182382107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001182382107 none CC(C)c1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 35, 30, 17, 30, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 34, 49, 49, 49, 49, 49, 49, 49, 49, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 17, 17, 4, 3, 3, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 35, 35] 50 rigid atoms, others: [11, 13, 15, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 164 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001182382107 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107 Building ZINC001182382107 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001182382107 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 24) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/24: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1) `ZINC001182382107.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182382107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001182382107 none CC(C)c1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 33, 32, 33, 33, 24, 15, 24, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 28, 47, 47, 47, 47, 47, 47, 47, 47, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 15, 15, 3, 3, 3, 1, 3, 3, 47, 47, 47, 47, 47, 47, 47, 47, 33, 33] 50 rigid atoms, others: [11, 13, 15, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 166 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 25) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/25: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1) `ZINC001182382107.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182382107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001182382107 none CC(C)c1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 35, 30, 17, 30, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 34, 49, 49, 49, 49, 49, 49, 49, 49, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 17, 17, 4, 3, 3, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 35, 35] 50 rigid atoms, others: [11, 13, 15, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 164 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 26) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/26: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1) `ZINC001182382107.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001182382107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001182382107 none CC(C)c1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 33, 32, 33, 33, 24, 15, 24, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 28, 47, 47, 47, 47, 47, 47, 47, 47, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 15, 15, 3, 3, 3, 1, 3, 3, 47, 47, 47, 47, 47, 47, 47, 47, 33, 33] 50 rigid atoms, others: [11, 13, 15, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 166 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 27) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/27: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1) `ZINC001182382107.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001182382107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001182382107 none CC(C)c1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 35, 30, 17, 30, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 34, 49, 49, 49, 49, 49, 49, 49, 49, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 17, 17, 4, 3, 3, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 35, 35] 50 rigid atoms, others: [11, 13, 15, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 164 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001182382107 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107 Building ZINC001182382107 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001182382107 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 24) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/24: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1) `ZINC001182382107.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182382107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001182382107 none CC(C)c1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 33, 32, 33, 33, 24, 15, 24, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 28, 47, 47, 47, 47, 47, 47, 47, 47, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 15, 15, 3, 3, 3, 1, 3, 3, 47, 47, 47, 47, 47, 47, 47, 47, 33, 33] 50 rigid atoms, others: [11, 13, 15, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 166 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 25) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/25: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1) `ZINC001182382107.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182382107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001182382107 none CC(C)c1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 35, 30, 17, 30, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 34, 49, 49, 49, 49, 49, 49, 49, 49, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 17, 17, 4, 3, 3, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 35, 35] 50 rigid atoms, others: [11, 13, 15, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 164 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 26) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/26: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1) `ZINC001182382107.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001182382107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001182382107 none CC(C)c1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 33, 32, 33, 33, 24, 15, 24, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 28, 47, 47, 47, 47, 47, 47, 47, 47, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 15, 15, 3, 3, 3, 1, 3, 3, 47, 47, 47, 47, 47, 47, 47, 47, 33, 33] 50 rigid atoms, others: [11, 13, 15, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 166 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 27) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/27: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1) `ZINC001182382107.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001182382107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001182382107 none CC(C)c1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 35, 30, 17, 30, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 34, 49, 49, 49, 49, 49, 49, 49, 49, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 17, 17, 4, 3, 3, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 35, 35] 50 rigid atoms, others: [11, 13, 15, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 164 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001182382107 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107 Building ZINC001182382107 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001182382107 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 24) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/24: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1) `ZINC001182382107.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182382107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001182382107 none CC(C)c1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 33, 32, 33, 33, 24, 15, 24, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 28, 47, 47, 47, 47, 47, 47, 47, 47, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 15, 15, 3, 3, 3, 1, 3, 3, 47, 47, 47, 47, 47, 47, 47, 47, 33, 33] 50 rigid atoms, others: [11, 13, 15, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 166 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 25) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/25: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1) `ZINC001182382107.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182382107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001182382107 none CC(C)c1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 35, 30, 17, 30, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 34, 49, 49, 49, 49, 49, 49, 49, 49, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 17, 17, 4, 3, 3, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 35, 35] 50 rigid atoms, others: [11, 13, 15, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 164 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 26) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/26: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1) `ZINC001182382107.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001182382107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001182382107 none CC(C)c1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 33, 32, 33, 33, 24, 15, 24, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 28, 47, 47, 47, 47, 47, 47, 47, 47, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 15, 15, 3, 3, 3, 1, 3, 3, 47, 47, 47, 47, 47, 47, 47, 47, 33, 33] 50 rigid atoms, others: [11, 13, 15, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 166 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 27) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/27: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1) `ZINC001182382107.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001182382107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001182382107 none CC(C)c1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 35, 30, 17, 30, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 34, 49, 49, 49, 49, 49, 49, 49, 49, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 17, 17, 4, 3, 3, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 35, 35] 50 rigid atoms, others: [11, 13, 15, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 164 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001182382107 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382107 Building ZINC001182382108 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001182382108 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 28) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/28 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/28' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1) `ZINC001182382108.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182382108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001182382108 none CC(C)c1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 35, 37, 35, 37, 37, 32, 18, 32, 4, 4, 1, 4, 1, 1, 1, 2, 2, 1, 2, 2, 36, 50, 50, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 18, 18, 4, 2, 2, 1, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 37, 37] 50 rigid atoms, others: [11, 13, 15, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 186 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 29) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/29 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/29' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1) `ZINC001182382108.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182382108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001182382108 none CC(C)c1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 25, 15, 25, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 30, 47, 47, 47, 47, 47, 47, 47, 47, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 15, 15, 4, 3, 3, 1, 3, 3, 47, 47, 47, 47, 47, 47, 47, 47, 32, 32] 50 rigid atoms, others: [11, 13, 15, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 157 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 30) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/30 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/30' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1) `ZINC001182382108.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001182382108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001182382108 none CC(C)c1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 35, 37, 35, 37, 37, 32, 18, 32, 4, 4, 1, 4, 1, 1, 1, 2, 2, 1, 2, 2, 36, 50, 50, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 18, 18, 4, 2, 2, 1, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 37, 37] 50 rigid atoms, others: [11, 13, 15, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 186 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 31) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/31 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/31' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1) `ZINC001182382108.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001182382108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001182382108 none CC(C)c1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 25, 15, 25, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 30, 47, 47, 47, 47, 47, 47, 47, 47, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 15, 15, 4, 3, 3, 1, 3, 3, 47, 47, 47, 47, 47, 47, 47, 47, 32, 32] 50 rigid atoms, others: [11, 13, 15, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 157 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001182382108 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108 Building ZINC001182382108 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001182382108 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 28) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/28: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1) `ZINC001182382108.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182382108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001182382108 none CC(C)c1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 35, 37, 35, 37, 37, 32, 18, 32, 4, 4, 1, 4, 1, 1, 1, 2, 2, 1, 2, 2, 36, 50, 50, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 18, 18, 4, 2, 2, 1, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 37, 37] 50 rigid atoms, others: [11, 13, 15, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 186 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 29) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/29: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1) `ZINC001182382108.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182382108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001182382108 none CC(C)c1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 25, 15, 25, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 30, 47, 47, 47, 47, 47, 47, 47, 47, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 15, 15, 4, 3, 3, 1, 3, 3, 47, 47, 47, 47, 47, 47, 47, 47, 32, 32] 50 rigid atoms, others: [11, 13, 15, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 157 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 30) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/30: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1) `ZINC001182382108.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001182382108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001182382108 none CC(C)c1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 35, 37, 35, 37, 37, 32, 18, 32, 4, 4, 1, 4, 1, 1, 1, 2, 2, 1, 2, 2, 36, 50, 50, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 18, 18, 4, 2, 2, 1, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 37, 37] 50 rigid atoms, others: [11, 13, 15, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 186 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 31) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/31: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1) `ZINC001182382108.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001182382108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001182382108 none CC(C)c1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 25, 15, 25, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 30, 47, 47, 47, 47, 47, 47, 47, 47, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 15, 15, 4, 3, 3, 1, 3, 3, 47, 47, 47, 47, 47, 47, 47, 47, 32, 32] 50 rigid atoms, others: [11, 13, 15, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 157 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001182382108 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108 Building ZINC001182382108 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001182382108 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 28) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/28: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1) `ZINC001182382108.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182382108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001182382108 none CC(C)c1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 35, 37, 35, 37, 37, 32, 18, 32, 4, 4, 1, 4, 1, 1, 1, 2, 2, 1, 2, 2, 36, 50, 50, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 18, 18, 4, 2, 2, 1, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 37, 37] 50 rigid atoms, others: [11, 13, 15, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 186 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 29) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/29: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1) `ZINC001182382108.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182382108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001182382108 none CC(C)c1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 25, 15, 25, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 30, 47, 47, 47, 47, 47, 47, 47, 47, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 15, 15, 4, 3, 3, 1, 3, 3, 47, 47, 47, 47, 47, 47, 47, 47, 32, 32] 50 rigid atoms, others: [11, 13, 15, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 157 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 30) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/30: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1) `ZINC001182382108.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001182382108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001182382108 none CC(C)c1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 35, 37, 35, 37, 37, 32, 18, 32, 4, 4, 1, 4, 1, 1, 1, 2, 2, 1, 2, 2, 36, 50, 50, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 18, 18, 4, 2, 2, 1, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 37, 37] 50 rigid atoms, others: [11, 13, 15, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 186 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 31) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/31: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1) `ZINC001182382108.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001182382108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001182382108 none CC(C)c1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 25, 15, 25, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 30, 47, 47, 47, 47, 47, 47, 47, 47, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 15, 15, 4, 3, 3, 1, 3, 3, 47, 47, 47, 47, 47, 47, 47, 47, 32, 32] 50 rigid atoms, others: [11, 13, 15, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 157 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001182382108 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108 Building ZINC001182382108 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001182382108 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 28) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/28: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1) `ZINC001182382108.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182382108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001182382108 none CC(C)c1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 35, 37, 35, 37, 37, 32, 18, 32, 4, 4, 1, 4, 1, 1, 1, 2, 2, 1, 2, 2, 36, 50, 50, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 18, 18, 4, 2, 2, 1, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 37, 37] 50 rigid atoms, others: [11, 13, 15, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 186 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 29) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/29: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1) `ZINC001182382108.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182382108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001182382108 none CC(C)c1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 25, 15, 25, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 30, 47, 47, 47, 47, 47, 47, 47, 47, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 15, 15, 4, 3, 3, 1, 3, 3, 47, 47, 47, 47, 47, 47, 47, 47, 32, 32] 50 rigid atoms, others: [11, 13, 15, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 157 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 30) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/30: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1) `ZINC001182382108.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001182382108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001182382108 none CC(C)c1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 35, 37, 35, 37, 37, 32, 18, 32, 4, 4, 1, 4, 1, 1, 1, 2, 2, 1, 2, 2, 36, 50, 50, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 18, 18, 4, 2, 2, 1, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 37, 37] 50 rigid atoms, others: [11, 13, 15, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 186 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 31) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/31: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1) `ZINC001182382108.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001182382108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001182382108 none CC(C)c1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 25, 15, 25, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 30, 47, 47, 47, 47, 47, 47, 47, 47, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 15, 15, 4, 3, 3, 1, 3, 3, 47, 47, 47, 47, 47, 47, 47, 47, 32, 32] 50 rigid atoms, others: [11, 13, 15, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 157 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001182382108 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182382108 Building ZINC001182668268 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182668268' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182668268 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182668268 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182668268/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182668268 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 32) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/32 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/32' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCCCCCC(=O)Nc1ccccc1NC(=O)[C@@]([O-])([SiH3])C1CC1)Nc1ccccc1) `ZINC001182668268.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182668268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182668268/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001182668268 none O=C(CCCCCCC(=O)Nc1ccccc1NC(=O)[C@@]([O-])([SiH3])C1CC1)Nc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 28, 8, 8, 8, 6, 6, 6, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 28, 28, 8, 6, 6, 6, 6, 2, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [54, 50, 18, 51, 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, 17, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 55, 56, 57, 58, 59, 60]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182668268 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182668268/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182668268 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 33) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/33 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/33' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCCCCCC(=O)Nc1ccccc1NC(=O)[C@]([O-])([SiH3])C1CC1)Nc1ccccc1) `ZINC001182668268.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182668268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182668268/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001182668268 none O=C(CCCCCCC(=O)Nc1ccccc1NC(=O)[C@]([O-])([SiH3])C1CC1)Nc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 27, 7, 7, 7, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 27, 27, 7, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [51, 54, 49, 50, 16, 17, 18, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 55, 56, 57, 58, 59, 60]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182668268 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001182668268 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182668268/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182668268/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182668268 Building ZINC001182668268 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182668268' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182668268 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182668268 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182668268/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182668268 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 32) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/32: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCCCCCC(=O)Nc1ccccc1NC(=O)[C@@]([O-])([SiH3])C1CC1)Nc1ccccc1) `ZINC001182668268.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182668268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182668268/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001182668268 none O=C(CCCCCCC(=O)Nc1ccccc1NC(=O)[C@@]([O-])([SiH3])C1CC1)Nc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 28, 8, 8, 8, 6, 6, 6, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 28, 28, 8, 6, 6, 6, 6, 2, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [54, 50, 18, 51, 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, 17, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 55, 56, 57, 58, 59, 60]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182668268 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182668268/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182668268 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 33) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/33: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCCCCCC(=O)Nc1ccccc1NC(=O)[C@]([O-])([SiH3])C1CC1)Nc1ccccc1) `ZINC001182668268.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182668268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182668268/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001182668268 none O=C(CCCCCCC(=O)Nc1ccccc1NC(=O)[C@]([O-])([SiH3])C1CC1)Nc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 27, 7, 7, 7, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 27, 27, 7, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [51, 54, 49, 50, 16, 17, 18, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 55, 56, 57, 58, 59, 60]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182668268 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001182668268 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182668268/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182668268/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182668268 Building ZINC001182668623 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182668623' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182668623 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182668623 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182668623/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182668623 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 34) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/34 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/34' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(c2ccc(Cl)cc2)(c2ccc(c3cn[nH]c3)cc2)CC1)[C@@]([O-])([SiH3])C1CC1) `ZINC001182668623.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182668623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182668623/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001182668623 none O=C(N1CCC(c2ccc(Cl)cc2)(c2ccc(c3cn[nH]c3)cc2)CC1)[C@@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 6, 1, 1, 1, 5, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 21, 21, 21, 21, 37, 37, 21, 21, 37, 37, 21, 35, 35, 22, 22, 42, 42, 42, 42, 42, 35, 35, 21, 21, 1, 1, 1, 4, 4, 21, 21, 21, 21, 37, 37, 37, 37, 35, 35, 42, 42, 35, 35, 21, 21, 21, 21, 4, 4, 4, 4, 4] 50 rigid atoms, others: [27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 192 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182668623 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182668623/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182668623 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 35) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/35 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/35' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(c2ccc(Cl)cc2)(c2ccc(c3cn[nH]c3)cc2)CC1)[C@]([O-])([SiH3])C1CC1) `ZINC001182668623.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182668623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182668623/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001182668623 none O=C(N1CCC(c2ccc(Cl)cc2)(c2ccc(c3cn[nH]c3)cc2)CC1)[C@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 6, 1, 1, 1, 5, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 24, 24, 24, 24, 33, 33, 24, 25, 33, 33, 24, 39, 39, 24, 24, 44, 44, 44, 44, 44, 39, 39, 24, 24, 1, 1, 1, 4, 4, 24, 24, 24, 24, 33, 33, 33, 33, 39, 39, 44, 44, 39, 39, 24, 24, 24, 24, 4, 4, 4, 4, 4] 50 rigid atoms, others: [27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 176 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182668623 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001182668623 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182668623/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182668623/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182668623 Building ZINC001182668623 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182668623' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182668623 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182668623 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182668623/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182668623 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 34) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/34: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(c2ccc(Cl)cc2)(c2ccc(c3cn[nH]c3)cc2)CC1)[C@@]([O-])([SiH3])C1CC1) `ZINC001182668623.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182668623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182668623/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001182668623 none O=C(N1CCC(c2ccc(Cl)cc2)(c2ccc(c3cn[nH]c3)cc2)CC1)[C@@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 6, 1, 1, 1, 5, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 21, 21, 21, 21, 37, 37, 21, 21, 37, 37, 21, 35, 35, 22, 22, 42, 42, 42, 42, 42, 35, 35, 21, 21, 1, 1, 1, 4, 4, 21, 21, 21, 21, 37, 37, 37, 37, 35, 35, 42, 42, 35, 35, 21, 21, 21, 21, 4, 4, 4, 4, 4] 50 rigid atoms, others: [27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 192 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182668623 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182668623/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182668623 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 35) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/35: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(c2ccc(Cl)cc2)(c2ccc(c3cn[nH]c3)cc2)CC1)[C@]([O-])([SiH3])C1CC1) `ZINC001182668623.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182668623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182668623/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001182668623 none O=C(N1CCC(c2ccc(Cl)cc2)(c2ccc(c3cn[nH]c3)cc2)CC1)[C@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 6, 1, 1, 1, 5, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 24, 24, 24, 24, 33, 33, 24, 25, 33, 33, 24, 39, 39, 24, 24, 44, 44, 44, 44, 44, 39, 39, 24, 24, 1, 1, 1, 4, 4, 24, 24, 24, 24, 33, 33, 33, 33, 39, 39, 44, 44, 39, 39, 24, 24, 24, 24, 4, 4, 4, 4, 4] 50 rigid atoms, others: [27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 176 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182668623 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001182668623 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182668623/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182668623/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182668623 Building ZINC001182893905 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182893905' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182893905 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182893905 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182893905/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182893905 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 36) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/36 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/36' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(n2c3ccccc3nc2C(F)(F)F)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182893905.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182893905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182893905/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001182893905 none O=C(N1CCC(n2c3ccccc3nc2C(F)(F)F)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 15, 15, 15, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 17, 27, 27, 27, 27, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 27, 27, 1, 1, 1, 4, 4, 1, 1, 4, 4, 27, 27, 27, 27, 27, 49, 49, 49, 49, 27, 27, 27, 27, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 86 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182893905 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182893905/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182893905 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 37) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/37 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/37' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(n2c3ccccc3nc2C(F)(F)F)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182893905.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182893905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182893905/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001182893905 none O=C(N1CCC(n2c3ccccc3nc2C(F)(F)F)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 15, 15, 15, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 15, 27, 27, 27, 27, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 27, 27, 1, 1, 1, 3, 3, 1, 1, 3, 3, 27, 27, 27, 27, 27, 49, 49, 49, 49, 27, 27, 27, 27, 3, 3, 3, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 89 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182893905 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001182893905 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182893905/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182893905/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182893905 Building ZINC001182893905 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182893905' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182893905 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182893905 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182893905/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182893905 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 36) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/36: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(n2c3ccccc3nc2C(F)(F)F)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182893905.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182893905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182893905/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001182893905 none O=C(N1CCC(n2c3ccccc3nc2C(F)(F)F)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 15, 15, 15, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 17, 27, 27, 27, 27, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 27, 27, 1, 1, 1, 4, 4, 1, 1, 4, 4, 27, 27, 27, 27, 27, 49, 49, 49, 49, 27, 27, 27, 27, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 86 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182893905 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182893905/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182893905 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 37) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/37: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(n2c3ccccc3nc2C(F)(F)F)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182893905.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182893905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182893905/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001182893905 none O=C(N1CCC(n2c3ccccc3nc2C(F)(F)F)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 15, 15, 15, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 15, 27, 27, 27, 27, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 27, 27, 1, 1, 1, 3, 3, 1, 1, 3, 3, 27, 27, 27, 27, 27, 49, 49, 49, 49, 27, 27, 27, 27, 3, 3, 3, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 89 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182893905 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001182893905 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182893905/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182893905/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182893905 Building ZINC001182894162 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182894162' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182894162 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182894162 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182894162/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182894162 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 38) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/38 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/38' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1csc(Cc2cccc(Br)c2)n1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182894162.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182894162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182894162/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001182894162 none O=C(Nc1csc(Cc2cccc(Br)c2)n1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 14, 1, 5, 1, 1, 1, 1, 1, 17, 1, 8, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 4, 4, 19, 50, 50, 50, 50, 50, 50, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 4, 19, 19, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182894162 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182894162/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182894162 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 39) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/39 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/39' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1csc(Cc2cccc(Br)c2)n1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182894162.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182894162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182894162/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001182894162 none O=C(Nc1csc(Cc2cccc(Br)c2)n1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 14, 1, 5, 1, 1, 1, 1, 1, 17, 1, 8, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 4, 4, 19, 50, 50, 36, 50, 50, 50, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 4, 19, 19, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182894162 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001182894162 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182894162/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182894162/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182894162 Building ZINC001182894162 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182894162' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182894162 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182894162 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182894162/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182894162 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 38) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/38: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1csc(Cc2cccc(Br)c2)n1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182894162.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182894162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182894162/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001182894162 none O=C(Nc1csc(Cc2cccc(Br)c2)n1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 14, 1, 5, 1, 1, 1, 1, 1, 17, 1, 8, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 4, 4, 19, 50, 50, 50, 50, 50, 50, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 4, 19, 19, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182894162 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182894162/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182894162 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 39) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/39: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1csc(Cc2cccc(Br)c2)n1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182894162.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182894162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182894162/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001182894162 none O=C(Nc1csc(Cc2cccc(Br)c2)n1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 14, 1, 5, 1, 1, 1, 1, 1, 17, 1, 8, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 4, 4, 19, 50, 50, 36, 50, 50, 50, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 4, 19, 19, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182894162 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001182894162 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182894162/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182894162/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182894162 Building ZINC001182894915 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182894915' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182894915 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182894915 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182894915/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182894915 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 40) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/40 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/40' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](OCc2ccccn2)[C@H](Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182894915.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182894915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182894915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001182894915 none O=C(N1CC[C@H](OCc2ccccn2)[C@H](Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 12, 5, 1, 1, 1, 1, 1, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 4, 9, 9, 9, 9, 9, 13, 23, 35, 35, 35, 35, 35, 9, 9, 9, 21, 23, 23, 21, 23, 23, 9, 1, 1, 1, 3, 3, 1, 3, 3, 3, 9, 9, 9, 9, 23, 23, 35, 35, 35, 35, 21, 21, 23, 23, 21, 23, 23, 9, 9, 3, 3, 3, 3] 50 rigid atoms, others: [1, 26, 27, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 167 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182894915 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182894915/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182894915 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 41) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/41 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/41' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](OCc2ccccn2)[C@H](Cc2ccccc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182894915.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182894915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182894915/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001182894915 none O=C(N1CC[C@H](OCc2ccccn2)[C@H](Cc2ccccc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 12, 5, 1, 1, 1, 1, 1, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 6, 8, 8, 8, 8, 8, 13, 27, 41, 41, 41, 41, 41, 8, 8, 8, 16, 18, 18, 16, 18, 18, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 27, 27, 41, 41, 41, 41, 16, 16, 18, 18, 16, 18, 18, 8, 8, 1, 1, 1, 1] 50 rigid atoms, others: [32, 1, 33, 53, 54, 55, 56, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 157 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182894915 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001182894915 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182894915/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182894915/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182894915 Building ZINC001182894915 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182894915' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182894915 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182894915 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182894915/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182894915 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 40) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/40: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](OCc2ccccn2)[C@H](Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182894915.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182894915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182894915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001182894915 none O=C(N1CC[C@H](OCc2ccccn2)[C@H](Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 12, 5, 1, 1, 1, 1, 1, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 4, 9, 9, 9, 9, 9, 13, 23, 35, 35, 35, 35, 35, 9, 9, 9, 21, 23, 23, 21, 23, 23, 9, 1, 1, 1, 3, 3, 1, 3, 3, 3, 9, 9, 9, 9, 23, 23, 35, 35, 35, 35, 21, 21, 23, 23, 21, 23, 23, 9, 9, 3, 3, 3, 3] 50 rigid atoms, others: [1, 26, 27, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 167 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182894915 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182894915/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182894915 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 41) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/41: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](OCc2ccccn2)[C@H](Cc2ccccc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182894915.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182894915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182894915/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001182894915 none O=C(N1CC[C@H](OCc2ccccn2)[C@H](Cc2ccccc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 12, 5, 1, 1, 1, 1, 1, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 6, 8, 8, 8, 8, 8, 13, 27, 41, 41, 41, 41, 41, 8, 8, 8, 16, 18, 18, 16, 18, 18, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 27, 27, 41, 41, 41, 41, 16, 16, 18, 18, 16, 18, 18, 8, 8, 1, 1, 1, 1] 50 rigid atoms, others: [32, 1, 33, 53, 54, 55, 56, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 157 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182894915 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001182894915 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182894915/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182894915/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182894915 Building ZINC001182896104 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896104' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896104 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182896104 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896104/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896104 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 42) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/42 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/42' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(N)cc1N(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1nccc(c2cccnc2)n1) `ZINC001182896104.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182896104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896104/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001182896104 none Cc1ccc(N)cc1N(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1nccc(c2cccnc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 5, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 5, 14, 14, 14, 14, 14, 45, 45, 45, 45, 45, 14, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 2, 2, 14, 14, 45, 45, 45, 45] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896104 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896104/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896104 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 43) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/43 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/43' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(N)cc1N(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1nccc(c2cccnc2)n1) `ZINC001182896104.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182896104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896104/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001182896104 none Cc1ccc(N)cc1N(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1nccc(c2cccnc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 5, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 5, 14, 14, 14, 14, 14, 43, 43, 43, 43, 43, 14, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 2, 2, 14, 14, 43, 43, 43, 43] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896104 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001182896104 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896104/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896104/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896104 Building ZINC001182896104 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896104' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896104 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182896104 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896104/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896104 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 42) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/42: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(N)cc1N(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1nccc(c2cccnc2)n1) `ZINC001182896104.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182896104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896104/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001182896104 none Cc1ccc(N)cc1N(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1nccc(c2cccnc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 5, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 5, 14, 14, 14, 14, 14, 45, 45, 45, 45, 45, 14, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 2, 2, 14, 14, 45, 45, 45, 45] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896104 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896104/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896104 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 43) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/43: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(N)cc1N(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1nccc(c2cccnc2)n1) `ZINC001182896104.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182896104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896104/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001182896104 none Cc1ccc(N)cc1N(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1nccc(c2cccnc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 5, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 5, 14, 14, 14, 14, 14, 43, 43, 43, 43, 43, 14, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 2, 2, 14, 14, 43, 43, 43, 43] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896104 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001182896104 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896104/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896104/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896104 Building ZINC001182896136 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001182896136 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 44) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/44 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/44' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182896136.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182896136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001182896136 none O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 28, 31, 31, 31, 31, 31, 44, 50, 50, 44, 50, 50, 44, 50, 50, 44, 50, 50, 31, 18, 1, 1, 1, 2, 2, 1, 1, 2, 2, 31, 31, 31, 31, 31, 31, 44, 50, 50, 44, 50, 50, 50, 50, 44, 50, 50, 31, 31, 28, 28, 2, 2, 2, 2] 50 rigid atoms, others: [1, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 45) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/45 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/45' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182896136.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182896136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001182896136 none O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 28, 31, 31, 31, 31, 31, 44, 50, 50, 44, 50, 50, 44, 50, 50, 44, 50, 50, 31, 18, 1, 1, 1, 2, 2, 1, 1, 2, 2, 31, 31, 31, 31, 31, 31, 44, 50, 50, 44, 50, 50, 50, 50, 44, 50, 50, 31, 31, 28, 28, 2, 2, 2, 2] 50 rigid atoms, others: [1, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 46) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/46 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/46' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182896136.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001182896136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001182896136 none O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 30, 32, 32, 32, 32, 32, 45, 50, 50, 47, 50, 50, 45, 50, 50, 45, 50, 50, 32, 23, 1, 1, 1, 2, 2, 1, 1, 2, 2, 32, 32, 32, 32, 32, 32, 45, 50, 50, 45, 50, 50, 50, 50, 45, 50, 50, 32, 32, 29, 30, 2, 2, 2, 2] 50 rigid atoms, others: [1, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 47) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/47 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/47' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182896136.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001182896136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001182896136 none O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 30, 32, 32, 32, 32, 32, 45, 50, 50, 47, 50, 50, 45, 50, 50, 45, 50, 50, 32, 23, 1, 1, 1, 2, 2, 1, 1, 2, 2, 32, 32, 32, 32, 32, 32, 45, 50, 50, 45, 50, 50, 50, 50, 45, 50, 50, 32, 32, 29, 30, 2, 2, 2, 2] 50 rigid atoms, others: [1, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001182896136 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136 Building ZINC001182896136 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001182896136 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 44) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/44: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182896136.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182896136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001182896136 none O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 28, 31, 31, 31, 31, 31, 44, 50, 50, 44, 50, 50, 44, 50, 50, 44, 50, 50, 31, 18, 1, 1, 1, 2, 2, 1, 1, 2, 2, 31, 31, 31, 31, 31, 31, 44, 50, 50, 44, 50, 50, 50, 50, 44, 50, 50, 31, 31, 28, 28, 2, 2, 2, 2] 50 rigid atoms, others: [1, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 45) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/45: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182896136.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182896136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001182896136 none O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 28, 31, 31, 31, 31, 31, 44, 50, 50, 44, 50, 50, 44, 50, 50, 44, 50, 50, 31, 18, 1, 1, 1, 2, 2, 1, 1, 2, 2, 31, 31, 31, 31, 31, 31, 44, 50, 50, 44, 50, 50, 50, 50, 44, 50, 50, 31, 31, 28, 28, 2, 2, 2, 2] 50 rigid atoms, others: [1, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 46) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/46: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182896136.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001182896136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001182896136 none O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 30, 32, 32, 32, 32, 32, 45, 50, 50, 47, 50, 50, 45, 50, 50, 45, 50, 50, 32, 23, 1, 1, 1, 2, 2, 1, 1, 2, 2, 32, 32, 32, 32, 32, 32, 45, 50, 50, 45, 50, 50, 50, 50, 45, 50, 50, 32, 32, 29, 30, 2, 2, 2, 2] 50 rigid atoms, others: [1, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 47) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/47: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182896136.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001182896136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001182896136 none O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 30, 32, 32, 32, 32, 32, 45, 50, 50, 47, 50, 50, 45, 50, 50, 45, 50, 50, 32, 23, 1, 1, 1, 2, 2, 1, 1, 2, 2, 32, 32, 32, 32, 32, 32, 45, 50, 50, 45, 50, 50, 50, 50, 45, 50, 50, 32, 32, 29, 30, 2, 2, 2, 2] 50 rigid atoms, others: [1, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001182896136 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136 Building ZINC001182896136 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001182896136 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 44) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/44: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182896136.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182896136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001182896136 none O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 28, 31, 31, 31, 31, 31, 44, 50, 50, 44, 50, 50, 44, 50, 50, 44, 50, 50, 31, 18, 1, 1, 1, 2, 2, 1, 1, 2, 2, 31, 31, 31, 31, 31, 31, 44, 50, 50, 44, 50, 50, 50, 50, 44, 50, 50, 31, 31, 28, 28, 2, 2, 2, 2] 50 rigid atoms, others: [1, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 45) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/45: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182896136.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182896136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001182896136 none O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 28, 31, 31, 31, 31, 31, 44, 50, 50, 44, 50, 50, 44, 50, 50, 44, 50, 50, 31, 18, 1, 1, 1, 2, 2, 1, 1, 2, 2, 31, 31, 31, 31, 31, 31, 44, 50, 50, 44, 50, 50, 50, 50, 44, 50, 50, 31, 31, 28, 28, 2, 2, 2, 2] 50 rigid atoms, others: [1, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 46) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/46: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182896136.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001182896136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001182896136 none O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 30, 32, 32, 32, 32, 32, 45, 50, 50, 47, 50, 50, 45, 50, 50, 45, 50, 50, 32, 23, 1, 1, 1, 2, 2, 1, 1, 2, 2, 32, 32, 32, 32, 32, 32, 45, 50, 50, 45, 50, 50, 50, 50, 45, 50, 50, 32, 32, 29, 30, 2, 2, 2, 2] 50 rigid atoms, others: [1, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 47) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/47: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182896136.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001182896136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001182896136 none O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 30, 32, 32, 32, 32, 32, 45, 50, 50, 47, 50, 50, 45, 50, 50, 45, 50, 50, 32, 23, 1, 1, 1, 2, 2, 1, 1, 2, 2, 32, 32, 32, 32, 32, 32, 45, 50, 50, 45, 50, 50, 50, 50, 45, 50, 50, 32, 32, 29, 30, 2, 2, 2, 2] 50 rigid atoms, others: [1, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001182896136 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136 Building ZINC001182896136 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001182896136 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 44) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/44: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182896136.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182896136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001182896136 none O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 28, 31, 31, 31, 31, 31, 44, 50, 50, 44, 50, 50, 44, 50, 50, 44, 50, 50, 31, 18, 1, 1, 1, 2, 2, 1, 1, 2, 2, 31, 31, 31, 31, 31, 31, 44, 50, 50, 44, 50, 50, 50, 50, 44, 50, 50, 31, 31, 28, 28, 2, 2, 2, 2] 50 rigid atoms, others: [1, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 45) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/45: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182896136.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182896136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001182896136 none O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 28, 31, 31, 31, 31, 31, 44, 50, 50, 44, 50, 50, 44, 50, 50, 44, 50, 50, 31, 18, 1, 1, 1, 2, 2, 1, 1, 2, 2, 31, 31, 31, 31, 31, 31, 44, 50, 50, 44, 50, 50, 50, 50, 44, 50, 50, 31, 31, 28, 28, 2, 2, 2, 2] 50 rigid atoms, others: [1, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 46) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/46: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182896136.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001182896136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001182896136 none O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 30, 32, 32, 32, 32, 32, 45, 50, 50, 47, 50, 50, 45, 50, 50, 45, 50, 50, 32, 23, 1, 1, 1, 2, 2, 1, 1, 2, 2, 32, 32, 32, 32, 32, 32, 45, 50, 50, 45, 50, 50, 50, 50, 45, 50, 50, 32, 32, 29, 30, 2, 2, 2, 2] 50 rigid atoms, others: [1, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 47) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/47: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182896136.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001182896136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001182896136 none O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 30, 32, 32, 32, 32, 32, 45, 50, 50, 47, 50, 50, 45, 50, 50, 45, 50, 50, 32, 23, 1, 1, 1, 2, 2, 1, 1, 2, 2, 32, 32, 32, 32, 32, 32, 45, 50, 50, 45, 50, 50, 50, 50, 45, 50, 50, 32, 32, 29, 30, 2, 2, 2, 2] 50 rigid atoms, others: [1, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001182896136 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896136 Building ZINC001182896217 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896217' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896217 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182896217 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896217/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896217 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 48) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/48 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/48' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(c1ccccc1)c1ccccc1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC001182896217.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182896217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896217/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001182896217 none O=C(N(c1ccccc1)c1ccccc1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 43, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 21, 6, 2, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 22, 1, 1, 1, 1, 22, 22, 22, 22] 50 rigid atoms, others: [46, 47, 48, 49, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50, 51, 52, 53]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896217 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896217/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896217 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 49) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/49 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/49' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(c1ccccc1)c1ccccc1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC001182896217.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182896217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896217/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001182896217 none O=C(N(c1ccccc1)c1ccccc1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 42, 49, 50, 50, 50, 50, 50, 49, 50, 50, 50, 50, 50, 20, 20, 19, 5, 2, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 20, 1, 1, 1, 1, 20, 20, 20, 20] 50 rigid atoms, others: [46, 47, 48, 49, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50, 51, 52, 53]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896217 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001182896217 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896217/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896217/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896217 Building ZINC001182896217 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896217' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896217 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182896217 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896217/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896217 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 48) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/48: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(c1ccccc1)c1ccccc1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC001182896217.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182896217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896217/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001182896217 none O=C(N(c1ccccc1)c1ccccc1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 43, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 21, 6, 2, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 22, 1, 1, 1, 1, 22, 22, 22, 22] 50 rigid atoms, others: [46, 47, 48, 49, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50, 51, 52, 53]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896217 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896217/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896217 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 49) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/49: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(c1ccccc1)c1ccccc1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC001182896217.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182896217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896217/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001182896217 none O=C(N(c1ccccc1)c1ccccc1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 42, 49, 50, 50, 50, 50, 50, 49, 50, 50, 50, 50, 50, 20, 20, 19, 5, 2, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 20, 1, 1, 1, 1, 20, 20, 20, 20] 50 rigid atoms, others: [46, 47, 48, 49, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50, 51, 52, 53]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896217 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001182896217 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896217/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896217/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896217 Building ZINC001182896429 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896429' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896429 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182896429 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896429/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896429 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 50) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/50 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/50' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(c2cc(=O)c3ccccc3o2)c1NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182896429.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182896429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896429/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001182896429 none COc1cccc(c2cc(=O)c3ccccc3o2)c1NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 13, 13, 13, 13, 13, 13, 13, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 18, 18, 18, 13, 13, 13, 46, 46, 46, 46, 46, 4, 3, 3, 3, 3] 50 rigid atoms, others: [20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896429 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896429/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896429 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 51) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/51 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/51' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(c2cc(=O)c3ccccc3o2)c1NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182896429.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182896429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896429/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001182896429 none COc1cccc(c2cc(=O)c3ccccc3o2)c1NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 13, 13, 13, 6, 13, 13, 13, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 18, 18, 18, 13, 13, 13, 46, 46, 46, 46, 46, 4, 3, 3, 3, 3] 50 rigid atoms, others: [20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896429 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001182896429 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896429/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896429/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896429 Building ZINC001182896429 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896429' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896429 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182896429 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896429/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896429 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 50) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/50: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(c2cc(=O)c3ccccc3o2)c1NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182896429.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182896429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896429/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001182896429 none COc1cccc(c2cc(=O)c3ccccc3o2)c1NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 13, 13, 13, 13, 13, 13, 13, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 18, 18, 18, 13, 13, 13, 46, 46, 46, 46, 46, 4, 3, 3, 3, 3] 50 rigid atoms, others: [20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896429 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896429/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896429 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 51) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/51: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(c2cc(=O)c3ccccc3o2)c1NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182896429.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182896429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896429/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001182896429 none COc1cccc(c2cc(=O)c3ccccc3o2)c1NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 13, 13, 13, 6, 13, 13, 13, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 18, 18, 18, 13, 13, 13, 46, 46, 46, 46, 46, 4, 3, 3, 3, 3] 50 rigid atoms, others: [20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896429 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001182896429 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896429/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896429/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896429 Building ZINC001182896498 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896498' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896498 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182896498 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896498/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896498 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 52) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/52 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/52' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)C1CCN(C(=O)OC(C)(C)C)CC1) `ZINC001182896498.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182896498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001182896498 none CC(C)(C)CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)C1CCN(C(=O)OC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 4, 4, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 5, 9, 9, 9, 9, 23, 23, 49, 50, 50, 50, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 128 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896498 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896498/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896498 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 53) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/53 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/53' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)CN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)C1CCN(C(=O)OC(C)(C)C)CC1) `ZINC001182896498.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182896498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896498/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001182896498 none CC(C)(C)CN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)C1CCN(C(=O)OC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 6, 6, 4, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 5, 9, 9, 9, 9, 22, 22, 49, 50, 50, 50, 9, 9, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 3, 3, 3, 3, 9, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 135 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896498 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001182896498 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896498/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896498/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896498 Building ZINC001182896498 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896498' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896498 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182896498 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896498/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896498 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 52) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/52: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)C1CCN(C(=O)OC(C)(C)C)CC1) `ZINC001182896498.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182896498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001182896498 none CC(C)(C)CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)C1CCN(C(=O)OC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 4, 4, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 5, 9, 9, 9, 9, 23, 23, 49, 50, 50, 50, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 128 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896498 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896498/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896498 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 53) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/53: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)CN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)C1CCN(C(=O)OC(C)(C)C)CC1) `ZINC001182896498.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182896498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896498/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001182896498 none CC(C)(C)CN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)C1CCN(C(=O)OC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 6, 6, 4, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 5, 9, 9, 9, 9, 22, 22, 49, 50, 50, 50, 9, 9, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 3, 3, 3, 3, 9, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 135 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896498 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001182896498 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896498/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896498/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896498 Building ZINC001182896791 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896791' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896791 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182896791 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896791/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896791 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 54) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/54 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/54' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1n1c(=O)c2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)ccc2nc1CF) `ZINC001182896791.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182896791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896791/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001182896791 none Cc1ccccc1n1c(=O)c2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)ccc2nc1CF NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 8, 1, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 32, 46, 46, 21, 21, 21, 21, 21, 21, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 21, 21, 21, 21, 21, 21, 30, 46, 46, 46, 46, 21, 46, 46, 21, 4, 3, 3, 3, 3, 21, 21, 30, 30] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896791 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896791/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896791 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 55) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/55 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/55' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1n1c(=O)c2cc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)ccc2nc1CF) `ZINC001182896791.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182896791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896791/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001182896791 none Cc1ccccc1n1c(=O)c2cc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)ccc2nc1CF NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 8, 1, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 21, 43, 43, 21, 21, 21, 21, 21, 21, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 21, 21, 21, 21, 21, 21, 32, 43, 43, 43, 43, 36, 43, 43, 21, 4, 3, 3, 3, 3, 21, 21, 32, 32] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896791 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001182896791 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896791/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896791/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896791 Building ZINC001182896791 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896791' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896791 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182896791 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896791/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896791 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 54) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/54: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1n1c(=O)c2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)ccc2nc1CF) `ZINC001182896791.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182896791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896791/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001182896791 none Cc1ccccc1n1c(=O)c2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)ccc2nc1CF NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 8, 1, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 32, 46, 46, 21, 21, 21, 21, 21, 21, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 21, 21, 21, 21, 21, 21, 30, 46, 46, 46, 46, 21, 46, 46, 21, 4, 3, 3, 3, 3, 21, 21, 30, 30] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896791 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896791/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896791 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 55) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/55: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1n1c(=O)c2cc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)ccc2nc1CF) `ZINC001182896791.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182896791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896791/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001182896791 none Cc1ccccc1n1c(=O)c2cc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)ccc2nc1CF NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 8, 1, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 21, 43, 43, 21, 21, 21, 21, 21, 21, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 21, 21, 21, 21, 21, 21, 32, 43, 43, 43, 43, 36, 43, 43, 21, 4, 3, 3, 3, 3, 21, 21, 32, 32] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896791 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001182896791 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896791/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896791/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896791 Building ZINC001182896815 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001182896815 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 56) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/56 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/56' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1ccccc1N(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)[C@H]1CC[N@](Cc2ccccc2)CC1) `ZINC001182896815.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182896815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001182896815 none Nc1ccccc1N(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)[C@H]1CC[N@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 7, 8, 8, 5, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 5, 25, 25, 25, 25, 25, 47, 48, 48, 47, 48, 48, 25, 25, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 25, 25, 25, 25, 47, 47, 48, 48, 48, 48, 48, 25, 25, 25, 25] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 214 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 57) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/57 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/57' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1ccccc1N(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)[C@H]1CC[N@@](Cc2ccccc2)CC1) `ZINC001182896815.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182896815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001182896815 none Nc1ccccc1N(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)[C@H]1CC[N@@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 7, 8, 8, 5, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 5, 27, 27, 27, 27, 27, 48, 48, 48, 48, 48, 48, 27, 27, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 27, 27, 27, 27, 48, 48, 48, 48, 48, 48, 48, 27, 27, 27, 27] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 208 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 58) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/58 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/58' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1ccccc1N(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)[C@H]1CC[N@](Cc2ccccc2)CC1) `ZINC001182896815.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001182896815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001182896815 none Nc1ccccc1N(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)[C@H]1CC[N@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 7, 8, 8, 5, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 5, 25, 25, 25, 25, 25, 48, 48, 48, 48, 48, 48, 25, 25, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 25, 25, 25, 25, 48, 48, 48, 48, 48, 48, 48, 25, 25, 25, 25] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 214 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 59) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/59 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/59' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1ccccc1N(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)[C@H]1CC[N@@](Cc2ccccc2)CC1) `ZINC001182896815.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001182896815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001182896815 none Nc1ccccc1N(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)[C@H]1CC[N@@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 7, 8, 8, 5, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 5, 25, 25, 25, 25, 25, 47, 48, 48, 48, 48, 48, 25, 25, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 25, 25, 25, 25, 47, 47, 48, 48, 48, 48, 48, 25, 25, 25, 25] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 210 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001182896815 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815 Building ZINC001182896815 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001182896815 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 56) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/56: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1ccccc1N(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)[C@H]1CC[N@](Cc2ccccc2)CC1) `ZINC001182896815.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182896815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001182896815 none Nc1ccccc1N(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)[C@H]1CC[N@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 7, 8, 8, 5, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 5, 25, 25, 25, 25, 25, 47, 48, 48, 47, 48, 48, 25, 25, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 25, 25, 25, 25, 47, 47, 48, 48, 48, 48, 48, 25, 25, 25, 25] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 214 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 57) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/57: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1ccccc1N(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)[C@H]1CC[N@@](Cc2ccccc2)CC1) `ZINC001182896815.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182896815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001182896815 none Nc1ccccc1N(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)[C@H]1CC[N@@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 7, 8, 8, 5, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 5, 27, 27, 27, 27, 27, 48, 48, 48, 48, 48, 48, 27, 27, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 27, 27, 27, 27, 48, 48, 48, 48, 48, 48, 48, 27, 27, 27, 27] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 208 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 58) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/58: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1ccccc1N(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)[C@H]1CC[N@](Cc2ccccc2)CC1) `ZINC001182896815.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001182896815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001182896815 none Nc1ccccc1N(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)[C@H]1CC[N@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 7, 8, 8, 5, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 5, 25, 25, 25, 25, 25, 48, 48, 48, 48, 48, 48, 25, 25, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 25, 25, 25, 25, 48, 48, 48, 48, 48, 48, 48, 25, 25, 25, 25] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 214 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 59) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/59: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1ccccc1N(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)[C@H]1CC[N@@](Cc2ccccc2)CC1) `ZINC001182896815.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001182896815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001182896815 none Nc1ccccc1N(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)[C@H]1CC[N@@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 7, 8, 8, 5, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 5, 25, 25, 25, 25, 25, 47, 48, 48, 48, 48, 48, 25, 25, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 25, 25, 25, 25, 47, 47, 48, 48, 48, 48, 48, 25, 25, 25, 25] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 210 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001182896815 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815 Building ZINC001182896815 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001182896815 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 56) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/56: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1ccccc1N(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)[C@H]1CC[N@](Cc2ccccc2)CC1) `ZINC001182896815.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182896815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001182896815 none Nc1ccccc1N(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)[C@H]1CC[N@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 7, 8, 8, 5, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 5, 25, 25, 25, 25, 25, 47, 48, 48, 47, 48, 48, 25, 25, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 25, 25, 25, 25, 47, 47, 48, 48, 48, 48, 48, 25, 25, 25, 25] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 214 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 57) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/57: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1ccccc1N(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)[C@H]1CC[N@@](Cc2ccccc2)CC1) `ZINC001182896815.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182896815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001182896815 none Nc1ccccc1N(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)[C@H]1CC[N@@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 7, 8, 8, 5, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 5, 27, 27, 27, 27, 27, 48, 48, 48, 48, 48, 48, 27, 27, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 27, 27, 27, 27, 48, 48, 48, 48, 48, 48, 48, 27, 27, 27, 27] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 208 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 58) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/58: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1ccccc1N(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)[C@H]1CC[N@](Cc2ccccc2)CC1) `ZINC001182896815.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001182896815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001182896815 none Nc1ccccc1N(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)[C@H]1CC[N@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 7, 8, 8, 5, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 5, 25, 25, 25, 25, 25, 48, 48, 48, 48, 48, 48, 25, 25, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 25, 25, 25, 25, 48, 48, 48, 48, 48, 48, 48, 25, 25, 25, 25] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 214 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 59) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/59: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1ccccc1N(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)[C@H]1CC[N@@](Cc2ccccc2)CC1) `ZINC001182896815.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001182896815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001182896815 none Nc1ccccc1N(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)[C@H]1CC[N@@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 7, 8, 8, 5, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 5, 25, 25, 25, 25, 25, 47, 48, 48, 48, 48, 48, 25, 25, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 25, 25, 25, 25, 47, 47, 48, 48, 48, 48, 48, 25, 25, 25, 25] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 210 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001182896815 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815 Building ZINC001182896815 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001182896815 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 56) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/56: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1ccccc1N(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)[C@H]1CC[N@](Cc2ccccc2)CC1) `ZINC001182896815.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182896815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001182896815 none Nc1ccccc1N(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)[C@H]1CC[N@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 7, 8, 8, 5, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 5, 25, 25, 25, 25, 25, 47, 48, 48, 47, 48, 48, 25, 25, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 25, 25, 25, 25, 47, 47, 48, 48, 48, 48, 48, 25, 25, 25, 25] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 214 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 57) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/57: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1ccccc1N(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)[C@H]1CC[N@@](Cc2ccccc2)CC1) `ZINC001182896815.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182896815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001182896815 none Nc1ccccc1N(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)[C@H]1CC[N@@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 7, 8, 8, 5, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 5, 27, 27, 27, 27, 27, 48, 48, 48, 48, 48, 48, 27, 27, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 27, 27, 27, 27, 48, 48, 48, 48, 48, 48, 48, 27, 27, 27, 27] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 208 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 58) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/58: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1ccccc1N(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)[C@H]1CC[N@](Cc2ccccc2)CC1) `ZINC001182896815.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001182896815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001182896815 none Nc1ccccc1N(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)[C@H]1CC[N@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 7, 8, 8, 5, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 5, 25, 25, 25, 25, 25, 48, 48, 48, 48, 48, 48, 25, 25, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 25, 25, 25, 25, 48, 48, 48, 48, 48, 48, 48, 25, 25, 25, 25] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 214 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 59) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/59: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1ccccc1N(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)[C@H]1CC[N@@](Cc2ccccc2)CC1) `ZINC001182896815.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001182896815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001182896815 none Nc1ccccc1N(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)[C@H]1CC[N@@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 7, 8, 8, 5, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 5, 25, 25, 25, 25, 25, 47, 48, 48, 48, 48, 48, 25, 25, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 25, 25, 25, 25, 47, 47, 48, 48, 48, 48, 48, 25, 25, 25, 25] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 210 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001182896815 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182896815 Building ZINC001182897273 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182897273' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182897273 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182897273 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182897273/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182897273 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 60) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/60 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/60' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(O)(C(F)(F)F)C(F)(F)F)ccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182897273.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182897273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182897273/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001182897273 none Cc1cc(C(O)(C(F)(F)F)C(F)(F)F)ccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'F', 'F', 'F', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 12, 5, 15, 15, 15, 5, 15, 15, 15, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 4, 4, 30, 30, 30, 30, 30, 30, 30, 30, 30, 12, 12, 4, 4, 1, 4, 1, 1, 1, 5, 5, 1, 1, 5, 5, 12, 12, 12, 12, 90, 12, 12, 4, 5, 5, 5, 5] 150 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182897273 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182897273/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182897273 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 61) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/61 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/61' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(O)(C(F)(F)F)C(F)(F)F)ccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182897273.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182897273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182897273/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001182897273 none Cc1cc(C(O)(C(F)(F)F)C(F)(F)F)ccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'F', 'F', 'F', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 12, 5, 15, 15, 15, 5, 15, 15, 15, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 4, 4, 32, 32, 32, 32, 32, 32, 32, 32, 32, 11, 11, 4, 4, 1, 4, 1, 1, 1, 5, 5, 1, 5, 5, 5, 11, 11, 11, 11, 97, 11, 11, 4, 5, 5, 5, 5] 150 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 244 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182897273 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001182897273 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182897273/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182897273/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182897273 Building ZINC001182897273 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182897273' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182897273 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182897273 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182897273/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182897273 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 60) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/60: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(O)(C(F)(F)F)C(F)(F)F)ccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182897273.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182897273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182897273/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001182897273 none Cc1cc(C(O)(C(F)(F)F)C(F)(F)F)ccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'F', 'F', 'F', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 12, 5, 15, 15, 15, 5, 15, 15, 15, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 4, 4, 30, 30, 30, 30, 30, 30, 30, 30, 30, 12, 12, 4, 4, 1, 4, 1, 1, 1, 5, 5, 1, 1, 5, 5, 12, 12, 12, 12, 90, 12, 12, 4, 5, 5, 5, 5] 150 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182897273 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182897273/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182897273 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 61) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/61: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(O)(C(F)(F)F)C(F)(F)F)ccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182897273.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182897273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182897273/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001182897273 none Cc1cc(C(O)(C(F)(F)F)C(F)(F)F)ccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'F', 'F', 'F', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 12, 5, 15, 15, 15, 5, 15, 15, 15, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 4, 4, 32, 32, 32, 32, 32, 32, 32, 32, 32, 11, 11, 4, 4, 1, 4, 1, 1, 1, 5, 5, 1, 5, 5, 5, 11, 11, 11, 11, 97, 11, 11, 4, 5, 5, 5, 5] 150 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 244 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182897273 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001182897273 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182897273/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182897273/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001182897273 Building ZINC001183093977 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183093977' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183093977 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183093977 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183093977/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183093977 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 62) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/62 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/62' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(Oc2ncccc2NC(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)c2c1CCC2) `ZINC001183093977.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183093977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183093977/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001183093977 none Cc1ccc(Oc2ncccc2NC(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)c2c1CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 12, 4, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 4, 4, 2, 2, 2, 5, 5, 5, 5, 5, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183093977 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183093977/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183093977 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 63) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/63 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/63' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(Oc2ncccc2NC(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)c2c1CCC2) `ZINC001183093977.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183093977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183093977/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001183093977 none Cc1ccc(Oc2ncccc2NC(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)c2c1CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 12, 4, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 4, 4, 4, 2, 2, 2, 5, 5, 5, 5, 5, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183093977 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183093977 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183093977/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183093977/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183093977 Building ZINC001183093977 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183093977' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183093977 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183093977 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183093977/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183093977 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 62) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/62: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(Oc2ncccc2NC(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)c2c1CCC2) `ZINC001183093977.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183093977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183093977/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001183093977 none Cc1ccc(Oc2ncccc2NC(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)c2c1CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 12, 4, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 4, 4, 2, 2, 2, 5, 5, 5, 5, 5, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183093977 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183093977/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183093977 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 63) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/63: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(Oc2ncccc2NC(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)c2c1CCC2) `ZINC001183093977.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183093977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183093977/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001183093977 none Cc1ccc(Oc2ncccc2NC(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)c2c1CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 12, 4, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 4, 4, 4, 2, 2, 2, 5, 5, 5, 5, 5, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183093977 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183093977 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183093977/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183093977/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183093977 Building ZINC001183095955 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183095955' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183095955 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183095955 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183095955/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183095955 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 64) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/64 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/64' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)c1c(NC(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)onc1c1ccccc1) `ZINC001183095955.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183095955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183095955/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001183095955 none CC(C)(C)OC(=O)c1c(NC(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)onc1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.2', 'C.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, 12, 1, 11, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 12, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 23, 23, 14, 4, 14, 4, 2, 2, 1, 2, 1, 1, 1, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 4, 4, 13, 13, 4, 13, 13, 23, 23, 23, 23, 23, 23, 23, 23, 23, 2, 3, 3, 7, 7, 7, 7, 7, 13, 13, 7, 13, 13] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183095955 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183095955/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183095955 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 65) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/65 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/65' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)c1c(NC(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)onc1c1ccccc1) `ZINC001183095955.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183095955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183095955/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001183095955 none CC(C)(C)OC(=O)c1c(NC(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)onc1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.2', 'C.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, 12, 1, 11, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 12, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 4, 14, 4, 2, 2, 1, 2, 1, 1, 1, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 4, 4, 12, 12, 4, 12, 12, 20, 20, 20, 20, 20, 20, 20, 20, 20, 2, 3, 3, 7, 7, 7, 7, 7, 12, 12, 4, 12, 12] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183095955 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183095955 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183095955/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183095955/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183095955 Building ZINC001183095955 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183095955' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183095955 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183095955 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183095955/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183095955 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 64) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/64: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)c1c(NC(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)onc1c1ccccc1) `ZINC001183095955.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183095955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183095955/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001183095955 none CC(C)(C)OC(=O)c1c(NC(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)onc1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.2', 'C.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, 12, 1, 11, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 12, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 23, 23, 14, 4, 14, 4, 2, 2, 1, 2, 1, 1, 1, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 4, 4, 13, 13, 4, 13, 13, 23, 23, 23, 23, 23, 23, 23, 23, 23, 2, 3, 3, 7, 7, 7, 7, 7, 13, 13, 7, 13, 13] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183095955 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183095955/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183095955 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 65) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/65: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)c1c(NC(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)onc1c1ccccc1) `ZINC001183095955.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183095955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183095955/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001183095955 none CC(C)(C)OC(=O)c1c(NC(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)onc1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.2', 'C.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, 12, 1, 11, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 12, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 4, 14, 4, 2, 2, 1, 2, 1, 1, 1, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 4, 4, 12, 12, 4, 12, 12, 20, 20, 20, 20, 20, 20, 20, 20, 20, 2, 3, 3, 7, 7, 7, 7, 7, 12, 12, 4, 12, 12] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183095955 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183095955 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183095955/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183095955/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183095955 Building ZINC001183096559 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183096559' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183096559 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183096559 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183096559/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183096559 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 66) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/66 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/66' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(CCC(=O)c1ccc2ccccc2c1)C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096559.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183096559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183096559/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001183096559 none CC(C)N(CCC(=O)c1ccc2ccccc2c1)C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 3, 4, 4, 4, 16, 16, 44, 44, 44, 44, 44, 44, 44, 44, 44, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 44, 44, 44, 44, 44, 44, 44, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 91 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183096559 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183096559/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183096559 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 67) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/67 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/67' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(CCC(=O)c1ccc2ccccc2c1)C(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096559.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183096559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183096559/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001183096559 none CC(C)N(CCC(=O)c1ccc2ccccc2c1)C(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 2, 4, 4, 4, 16, 16, 43, 43, 43, 43, 43, 43, 43, 43, 43, 1, 2, 1, 1, 1, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 43, 43, 43, 43, 43, 43, 43, 4, 4, 5, 5, 5, 5, 5] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 98 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183096559 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183096559 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183096559/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183096559/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183096559 Building ZINC001183096559 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183096559' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183096559 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183096559 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183096559/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183096559 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 66) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/66: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(CCC(=O)c1ccc2ccccc2c1)C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096559.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183096559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183096559/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001183096559 none CC(C)N(CCC(=O)c1ccc2ccccc2c1)C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 3, 4, 4, 4, 16, 16, 44, 44, 44, 44, 44, 44, 44, 44, 44, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 44, 44, 44, 44, 44, 44, 44, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 91 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183096559 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183096559/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183096559 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 67) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/67: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(CCC(=O)c1ccc2ccccc2c1)C(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096559.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183096559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183096559/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001183096559 none CC(C)N(CCC(=O)c1ccc2ccccc2c1)C(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 2, 4, 4, 4, 16, 16, 43, 43, 43, 43, 43, 43, 43, 43, 43, 1, 2, 1, 1, 1, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 43, 43, 43, 43, 43, 43, 43, 4, 4, 5, 5, 5, 5, 5] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 98 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183096559 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183096559 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183096559/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183096559/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183096559 Building ZINC001183097433 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097433' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097433 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183097433 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097433/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097433 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 68) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/68 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/68' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(c2ccc(OC(F)(F)F)cc2)CC1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097433.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183097433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097433/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001183097433 none O=C(N1CCC(c2ccc(OC(F)(F)F)cc2)CC1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 3, 3, 3, 6, 6, 3, 5, 27, 27, 27, 27, 6, 6, 3, 3, 1, 1, 1, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 3, 3, 6, 6, 6, 6, 3, 3, 3, 3, 7, 7, 9, 9, 9, 9, 9] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097433 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097433/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097433 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 69) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/69 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/69' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(c2ccc(OC(F)(F)F)cc2)CC1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097433.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183097433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097433/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001183097433 none O=C(N1CCC(c2ccc(OC(F)(F)F)cc2)CC1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 3, 3, 3, 3, 8, 8, 3, 6, 25, 28, 29, 29, 8, 8, 3, 3, 1, 1, 1, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 3, 3, 8, 8, 8, 8, 3, 3, 3, 3, 7, 7, 10, 10, 10, 10, 10] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 98 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097433 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183097433 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097433/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097433/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097433 Building ZINC001183097433 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097433' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097433 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183097433 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097433/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097433 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 68) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/68: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(c2ccc(OC(F)(F)F)cc2)CC1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097433.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183097433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097433/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001183097433 none O=C(N1CCC(c2ccc(OC(F)(F)F)cc2)CC1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 3, 3, 3, 6, 6, 3, 5, 27, 27, 27, 27, 6, 6, 3, 3, 1, 1, 1, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 3, 3, 6, 6, 6, 6, 3, 3, 3, 3, 7, 7, 9, 9, 9, 9, 9] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097433 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097433/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097433 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 69) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/69: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(c2ccc(OC(F)(F)F)cc2)CC1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097433.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183097433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097433/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001183097433 none O=C(N1CCC(c2ccc(OC(F)(F)F)cc2)CC1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 3, 3, 3, 3, 8, 8, 3, 6, 25, 28, 29, 29, 8, 8, 3, 3, 1, 1, 1, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 3, 3, 8, 8, 8, 8, 3, 3, 3, 3, 7, 7, 10, 10, 10, 10, 10] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 98 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097433 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183097433 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097433/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097433/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097433 Building ZINC001183097754 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097754' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097754 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183097754 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097754/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097754 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 70) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/70 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/70' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]([C@@H](Oc1ccccc1)c1ccccc1)N(C)C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097754.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183097754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001183097754 none C[C@@H]([C@@H](Oc1ccccc1)c1ccccc1)N(C)C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 3, 10, 10, 17, 17, 25, 33, 33, 25, 33, 33, 17, 17, 17, 17, 17, 17, 2, 3, 1, 2, 1, 1, 1, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 10, 10, 10, 33, 33, 25, 33, 33, 17, 17, 17, 17, 17, 3, 3, 3, 8, 8, 13, 13, 13, 13, 13] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 164 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097754 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097754/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097754 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 71) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/71 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/71' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]([C@@H](Oc1ccccc1)c1ccccc1)N(C)C(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097754.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183097754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097754/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001183097754 none C[C@@H]([C@@H](Oc1ccccc1)c1ccccc1)N(C)C(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 11, 11, 20, 20, 29, 32, 32, 29, 32, 32, 20, 21, 21, 20, 21, 21, 2, 3, 1, 2, 1, 1, 1, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11, 11, 11, 32, 32, 29, 32, 32, 21, 21, 20, 21, 21, 3, 3, 3, 7, 7, 12, 12, 12, 12, 12] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 144 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097754 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183097754 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097754/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097754/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097754 Building ZINC001183097754 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097754' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097754 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183097754 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097754/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097754 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 70) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/70: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]([C@@H](Oc1ccccc1)c1ccccc1)N(C)C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097754.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183097754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001183097754 none C[C@@H]([C@@H](Oc1ccccc1)c1ccccc1)N(C)C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 3, 10, 10, 17, 17, 25, 33, 33, 25, 33, 33, 17, 17, 17, 17, 17, 17, 2, 3, 1, 2, 1, 1, 1, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 10, 10, 10, 33, 33, 25, 33, 33, 17, 17, 17, 17, 17, 3, 3, 3, 8, 8, 13, 13, 13, 13, 13] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 164 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097754 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097754/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097754 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 71) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/71: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]([C@@H](Oc1ccccc1)c1ccccc1)N(C)C(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097754.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183097754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097754/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001183097754 none C[C@@H]([C@@H](Oc1ccccc1)c1ccccc1)N(C)C(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 11, 11, 20, 20, 29, 32, 32, 29, 32, 32, 20, 21, 21, 20, 21, 21, 2, 3, 1, 2, 1, 1, 1, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11, 11, 11, 32, 32, 29, 32, 32, 21, 21, 20, 21, 21, 3, 3, 3, 7, 7, 12, 12, 12, 12, 12] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 144 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097754 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183097754 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097754/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097754/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097754 Building ZINC001183097757 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097757' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097757 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183097757 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097757/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097757 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 72) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/72 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/72' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]([C@H](Oc1ccccc1)c1ccccc1)N(C)C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097757.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183097757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001183097757 none C[C@H]([C@H](Oc1ccccc1)c1ccccc1)N(C)C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 3, 9, 9, 18, 18, 27, 31, 31, 27, 31, 31, 18, 18, 18, 18, 18, 18, 2, 3, 1, 2, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 9, 9, 9, 31, 31, 27, 31, 31, 18, 18, 18, 18, 18, 3, 3, 3, 7, 7, 11, 11, 11, 11, 11] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 143 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097757 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097757/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097757 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 73) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/73 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/73' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]([C@H](Oc1ccccc1)c1ccccc1)N(C)C(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097757.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183097757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097757/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001183097757 none C[C@H]([C@H](Oc1ccccc1)c1ccccc1)N(C)C(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 3, 10, 10, 15, 15, 24, 30, 30, 27, 30, 30, 15, 15, 15, 15, 15, 15, 2, 3, 1, 2, 1, 1, 1, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 10, 10, 10, 30, 30, 30, 30, 30, 15, 15, 15, 15, 15, 3, 3, 3, 8, 8, 13, 13, 13, 13, 13] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 143 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097757 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183097757 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097757/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097757/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097757 Building ZINC001183097757 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097757' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097757 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183097757 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097757/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097757 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 72) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/72: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]([C@H](Oc1ccccc1)c1ccccc1)N(C)C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097757.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183097757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001183097757 none C[C@H]([C@H](Oc1ccccc1)c1ccccc1)N(C)C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 3, 9, 9, 18, 18, 27, 31, 31, 27, 31, 31, 18, 18, 18, 18, 18, 18, 2, 3, 1, 2, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 9, 9, 9, 31, 31, 27, 31, 31, 18, 18, 18, 18, 18, 3, 3, 3, 7, 7, 11, 11, 11, 11, 11] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 143 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097757 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097757/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097757 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 73) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/73: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]([C@H](Oc1ccccc1)c1ccccc1)N(C)C(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097757.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183097757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097757/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001183097757 none C[C@H]([C@H](Oc1ccccc1)c1ccccc1)N(C)C(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 3, 10, 10, 15, 15, 24, 30, 30, 27, 30, 30, 15, 15, 15, 15, 15, 15, 2, 3, 1, 2, 1, 1, 1, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 10, 10, 10, 30, 30, 30, 30, 30, 15, 15, 15, 15, 15, 3, 3, 3, 8, 8, 13, 13, 13, 13, 13] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 143 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097757 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183097757 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097757/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097757/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097757 Building ZINC001183097759 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097759' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097759 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183097759 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097759/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097759 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 74) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/74 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/74' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]([C@@H](Oc1ccccc1)c1ccccc1)N(C)C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097759.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183097759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097759/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001183097759 none C[C@H]([C@@H](Oc1ccccc1)c1ccccc1)N(C)C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 9, 9, 13, 13, 20, 27, 27, 20, 27, 27, 13, 13, 13, 13, 13, 13, 3, 4, 1, 3, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 9, 9, 9, 27, 27, 20, 27, 27, 13, 13, 13, 13, 13, 4, 4, 4, 7, 7, 11, 11, 11, 11, 11] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 129 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097759 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097759/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097759 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 75) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/75 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/75' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]([C@@H](Oc1ccccc1)c1ccccc1)N(C)C(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097759.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183097759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097759/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001183097759 none C[C@H]([C@@H](Oc1ccccc1)c1ccccc1)N(C)C(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 13, 13, 18, 27, 27, 22, 27, 27, 13, 13, 13, 13, 13, 13, 3, 4, 1, 3, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 10, 10, 10, 27, 27, 27, 27, 27, 13, 13, 13, 13, 13, 4, 4, 4, 7, 7, 11, 11, 11, 11, 11] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 131 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097759 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183097759 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097759/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097759/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097759 Building ZINC001183097759 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097759' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097759 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183097759 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097759/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097759 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 74) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/74: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]([C@@H](Oc1ccccc1)c1ccccc1)N(C)C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097759.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183097759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097759/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001183097759 none C[C@H]([C@@H](Oc1ccccc1)c1ccccc1)N(C)C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 9, 9, 13, 13, 20, 27, 27, 20, 27, 27, 13, 13, 13, 13, 13, 13, 3, 4, 1, 3, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 9, 9, 9, 27, 27, 20, 27, 27, 13, 13, 13, 13, 13, 4, 4, 4, 7, 7, 11, 11, 11, 11, 11] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 129 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097759 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097759/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097759 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 75) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/75: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]([C@@H](Oc1ccccc1)c1ccccc1)N(C)C(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097759.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183097759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097759/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001183097759 none C[C@H]([C@@H](Oc1ccccc1)c1ccccc1)N(C)C(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 13, 13, 18, 27, 27, 22, 27, 27, 13, 13, 13, 13, 13, 13, 3, 4, 1, 3, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 10, 10, 10, 27, 27, 27, 27, 27, 13, 13, 13, 13, 13, 4, 4, 4, 7, 7, 11, 11, 11, 11, 11] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 131 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097759 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183097759 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097759/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097759/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097759 Building ZINC001183097761 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097761' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097761 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183097761 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097761/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097761 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 76) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/76 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/76' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]([C@H](Oc1ccccc1)c1ccccc1)N(C)C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097761.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183097761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001183097761 none C[C@@H]([C@H](Oc1ccccc1)c1ccccc1)N(C)C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 13, 13, 19, 28, 28, 19, 28, 28, 13, 13, 13, 13, 13, 13, 3, 4, 1, 3, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 10, 10, 10, 28, 28, 19, 28, 28, 13, 13, 13, 13, 13, 4, 4, 4, 7, 7, 11, 11, 11, 11, 11] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 127 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097761 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097761/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097761 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 77) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/77 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/77' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]([C@H](Oc1ccccc1)c1ccccc1)N(C)C(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097761.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183097761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097761/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001183097761 none C[C@@H]([C@H](Oc1ccccc1)c1ccccc1)N(C)C(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 12, 12, 20, 27, 27, 20, 27, 27, 12, 12, 12, 12, 12, 12, 3, 4, 1, 3, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 10, 10, 10, 27, 27, 20, 27, 27, 12, 12, 12, 12, 12, 4, 4, 4, 7, 7, 11, 11, 11, 11, 11] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 123 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097761 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183097761 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097761/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097761/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097761 Building ZINC001183097761 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097761' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097761 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183097761 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097761/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097761 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 76) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/76: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]([C@H](Oc1ccccc1)c1ccccc1)N(C)C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097761.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183097761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001183097761 none C[C@@H]([C@H](Oc1ccccc1)c1ccccc1)N(C)C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 13, 13, 19, 28, 28, 19, 28, 28, 13, 13, 13, 13, 13, 13, 3, 4, 1, 3, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 10, 10, 10, 28, 28, 19, 28, 28, 13, 13, 13, 13, 13, 4, 4, 4, 7, 7, 11, 11, 11, 11, 11] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 127 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097761 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097761/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097761 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 77) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/77: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]([C@H](Oc1ccccc1)c1ccccc1)N(C)C(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097761.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183097761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097761/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001183097761 none C[C@@H]([C@H](Oc1ccccc1)c1ccccc1)N(C)C(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 12, 12, 20, 27, 27, 20, 27, 27, 12, 12, 12, 12, 12, 12, 3, 4, 1, 3, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 10, 10, 10, 27, 27, 20, 27, 27, 12, 12, 12, 12, 12, 4, 4, 4, 7, 7, 11, 11, 11, 11, 11] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 123 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097761 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183097761 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097761/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097761/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183097761 Building ZINC001183098181 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183098181' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183098181 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183098181 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183098181/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183098181 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 78) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/78 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/78' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(C(F)(F)F)ccc1C(=O)C(F)(F)F)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183098181.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183098181.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183098181/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001183098181 none O=C(Nc1cc(C(F)(F)F)ccc1C(=O)C(F)(F)F)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 11, 5, 15, 15, 15, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 8, 8, 8, 8, 4, 8, 8, 8, 25, 25, 25, 25, 25, 1, 1, 1, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 8, 8, 4, 4, 7, 7, 7, 7, 7] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183098181 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183098181/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183098181 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 79) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/79 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/79' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(C(F)(F)F)ccc1C(=O)C(F)(F)F)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183098181.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183098181.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183098181/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001183098181 none O=C(Nc1cc(C(F)(F)F)ccc1C(=O)C(F)(F)F)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 11, 5, 15, 15, 15, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 1, 1, 1, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 8, 8, 8, 4, 4, 8, 8, 8, 8, 8] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183098181 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183098181 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183098181/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183098181/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183098181 Building ZINC001183098181 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183098181' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183098181 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183098181 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183098181/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183098181 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 78) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/78: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(C(F)(F)F)ccc1C(=O)C(F)(F)F)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183098181.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183098181.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183098181/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001183098181 none O=C(Nc1cc(C(F)(F)F)ccc1C(=O)C(F)(F)F)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 11, 5, 15, 15, 15, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 8, 8, 8, 8, 4, 8, 8, 8, 25, 25, 25, 25, 25, 1, 1, 1, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 8, 8, 4, 4, 7, 7, 7, 7, 7] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183098181 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183098181/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183098181 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 79) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/79: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(C(F)(F)F)ccc1C(=O)C(F)(F)F)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183098181.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183098181.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183098181/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001183098181 none O=C(Nc1cc(C(F)(F)F)ccc1C(=O)C(F)(F)F)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 11, 5, 15, 15, 15, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 1, 1, 1, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 8, 8, 8, 4, 4, 8, 8, 8, 8, 8] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183098181 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183098181 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183098181/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183098181/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183098181 Building ZINC001183098912 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183098912' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183098912 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183098912 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183098912/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183098912 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 80) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/80 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/80' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOP(=O)(Cc1ccc(NC(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)cc1)OCC) `ZINC001183098912.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183098912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183098912/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001183098912 none CCOP(=O)(Cc1ccc(NC(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)cc1)OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'P.3', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 13, 11, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 29, 20, 17, 20, 2, 2, 9, 9, 2, 2, 1, 2, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 20, 30, 30, 30, 30, 30, 30, 30, 17, 17, 9, 9, 2, 2, 2, 4, 4, 4, 4, 4, 9, 9, 30, 30, 30, 30, 30] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183098912 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183098912/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183098912 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 81) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/81 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/81' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOP(=O)(Cc1ccc(NC(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)cc1)OCC) `ZINC001183098912.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183098912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183098912/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001183098912 none CCOP(=O)(Cc1ccc(NC(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)cc1)OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'P.3', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 13, 11, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 18, 15, 18, 8, 5, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 18, 26, 27, 27, 27, 27, 27, 27, 15, 15, 8, 8, 2, 2, 2, 4, 4, 4, 4, 4, 8, 8, 27, 27, 27, 27, 27] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183098912 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183098912 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183098912/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183098912/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183098912 Building ZINC001183098912 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183098912' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183098912 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183098912 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183098912/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183098912 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 80) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/80: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOP(=O)(Cc1ccc(NC(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)cc1)OCC) `ZINC001183098912.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183098912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183098912/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001183098912 none CCOP(=O)(Cc1ccc(NC(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)cc1)OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'P.3', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 13, 11, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 29, 20, 17, 20, 2, 2, 9, 9, 2, 2, 1, 2, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 20, 30, 30, 30, 30, 30, 30, 30, 17, 17, 9, 9, 2, 2, 2, 4, 4, 4, 4, 4, 9, 9, 30, 30, 30, 30, 30] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183098912 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183098912/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183098912 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 81) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/81: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOP(=O)(Cc1ccc(NC(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)cc1)OCC) `ZINC001183098912.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183098912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183098912/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001183098912 none CCOP(=O)(Cc1ccc(NC(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)cc1)OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'P.3', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 13, 11, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 18, 15, 18, 8, 5, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 18, 26, 27, 27, 27, 27, 27, 27, 15, 15, 8, 8, 2, 2, 2, 4, 4, 4, 4, 4, 8, 8, 27, 27, 27, 27, 27] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183098912 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183098912 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183098912/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183098912/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183098912 Building ZINC001183099005 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099005' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099005 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183099005 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099005/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099005 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 82) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/82 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/82' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Br)cc1OC(F)(F)F)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183099005.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183099005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099005/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001183099005 none O=C(Nc1ccc(Br)cc1OC(F)(F)F)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 17, 1, 1, 12, 5, 15, 15, 15, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 6, 8, 8, 8, 8, 26, 29, 29, 29, 1, 1, 1, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 8, 8, 3, 3, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099005 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099005/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099005 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 83) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/83 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/83' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Br)cc1OC(F)(F)F)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183099005.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183099005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099005/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001183099005 none O=C(Nc1ccc(Br)cc1OC(F)(F)F)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 17, 1, 1, 12, 5, 15, 15, 15, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 6, 8, 8, 8, 8, 26, 29, 29, 29, 1, 1, 1, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 8, 8, 3, 3, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099005 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183099005 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099005/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099005/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099005 Building ZINC001183099005 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099005' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099005 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183099005 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099005/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099005 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 82) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/82: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Br)cc1OC(F)(F)F)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183099005.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183099005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099005/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001183099005 none O=C(Nc1ccc(Br)cc1OC(F)(F)F)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 17, 1, 1, 12, 5, 15, 15, 15, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 6, 8, 8, 8, 8, 26, 29, 29, 29, 1, 1, 1, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 8, 8, 3, 3, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099005 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099005/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099005 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 83) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/83: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Br)cc1OC(F)(F)F)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183099005.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183099005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099005/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001183099005 none O=C(Nc1ccc(Br)cc1OC(F)(F)F)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 17, 1, 1, 12, 5, 15, 15, 15, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 6, 8, 8, 8, 8, 26, 29, 29, 29, 1, 1, 1, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 8, 8, 3, 3, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099005 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183099005 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099005/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099005/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099005 Building ZINC001183099008 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099008' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099008 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183099008 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099008/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099008 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 84) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/84 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/84' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCC(C)(C)c1ccc(NC(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)cc1) `ZINC001183099008.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183099008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099008/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001183099008 none CC(C)(C)OC(=O)NCC(C)(C)c1ccc(NC(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 27, 32, 15, 11, 2, 11, 11, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 32, 32, 32, 32, 32, 32, 32, 32, 32, 27, 15, 15, 11, 12, 11, 11, 11, 13, 8, 8, 2, 2, 2, 4, 4, 4, 4, 4, 8, 8] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099008 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099008/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099008 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 85) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/85 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/85' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCC(C)(C)c1ccc(NC(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)cc1) `ZINC001183099008.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183099008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099008/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001183099008 none CC(C)(C)OC(=O)NCC(C)(C)c1ccc(NC(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 26, 31, 14, 13, 7, 13, 13, 4, 7, 7, 2, 2, 1, 2, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 31, 31, 31, 31, 31, 31, 31, 31, 31, 26, 14, 14, 13, 13, 13, 13, 13, 13, 7, 7, 2, 2, 2, 3, 3, 3, 3, 3, 7, 7] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099008 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183099008 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099008/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099008/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099008 Building ZINC001183099008 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099008' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099008 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183099008 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099008/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099008 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 84) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/84: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCC(C)(C)c1ccc(NC(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)cc1) `ZINC001183099008.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183099008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099008/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001183099008 none CC(C)(C)OC(=O)NCC(C)(C)c1ccc(NC(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 27, 32, 15, 11, 2, 11, 11, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 32, 32, 32, 32, 32, 32, 32, 32, 32, 27, 15, 15, 11, 12, 11, 11, 11, 13, 8, 8, 2, 2, 2, 4, 4, 4, 4, 4, 8, 8] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099008 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099008/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099008 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 85) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/85: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCC(C)(C)c1ccc(NC(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)cc1) `ZINC001183099008.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183099008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099008/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001183099008 none CC(C)(C)OC(=O)NCC(C)(C)c1ccc(NC(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 26, 31, 14, 13, 7, 13, 13, 4, 7, 7, 2, 2, 1, 2, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 31, 31, 31, 31, 31, 31, 31, 31, 31, 26, 14, 14, 13, 13, 13, 13, 13, 13, 7, 7, 2, 2, 2, 3, 3, 3, 3, 3, 7, 7] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099008 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183099008 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099008/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099008/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099008 Building ZINC001183099028 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099028' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099028 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183099028 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099028/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099028 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 86) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/86 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/86' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)c(C(=O)c2ccc(Cl)cc2)c1) `ZINC001183099028.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183099028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001183099028 none COc1ccc(NC(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)c(C(=O)c2ccc(Cl)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 11, 11, 11, 11, 3, 3, 1, 3, 1, 1, 1, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 11, 11, 17, 17, 26, 26, 18, 26, 26, 26, 11, 15, 15, 15, 11, 11, 3, 5, 5, 10, 10, 10, 10, 10, 26, 26, 26, 26, 11] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099028 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099028/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099028 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 87) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/87 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/87' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)c(C(=O)c2ccc(Cl)cc2)c1) `ZINC001183099028.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183099028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099028/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001183099028 none COc1ccc(NC(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)c(C(=O)c2ccc(Cl)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 11, 11, 11, 11, 3, 3, 1, 3, 1, 1, 1, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 11, 11, 17, 17, 26, 26, 17, 18, 26, 26, 11, 15, 15, 15, 11, 11, 3, 5, 5, 10, 10, 10, 10, 10, 26, 26, 26, 26, 11] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099028 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183099028 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099028/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099028/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099028 Building ZINC001183099028 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099028' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099028 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183099028 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099028/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099028 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 86) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/86: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)c(C(=O)c2ccc(Cl)cc2)c1) `ZINC001183099028.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183099028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001183099028 none COc1ccc(NC(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)c(C(=O)c2ccc(Cl)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 11, 11, 11, 11, 3, 3, 1, 3, 1, 1, 1, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 11, 11, 17, 17, 26, 26, 18, 26, 26, 26, 11, 15, 15, 15, 11, 11, 3, 5, 5, 10, 10, 10, 10, 10, 26, 26, 26, 26, 11] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099028 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099028/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099028 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 87) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/87: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)c(C(=O)c2ccc(Cl)cc2)c1) `ZINC001183099028.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183099028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099028/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001183099028 none COc1ccc(NC(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)c(C(=O)c2ccc(Cl)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 11, 11, 11, 11, 3, 3, 1, 3, 1, 1, 1, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 11, 11, 17, 17, 26, 26, 17, 18, 26, 26, 11, 15, 15, 15, 11, 11, 3, 5, 5, 10, 10, 10, 10, 10, 26, 26, 26, 26, 11] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099028 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183099028 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099028/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099028/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099028 Building ZINC001183099053 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099053' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099053 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183099053 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099053/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099053 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 88) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/88 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/88' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCc2ccc(NC(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)cc21) `ZINC001183099053.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183099053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099053/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001183099053 none CC(C)(C)OC(=O)N1CCCc2ccc(NC(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 34, 24, 34, 24, 24, 24, 24, 24, 24, 13, 2, 2, 1, 2, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 16, 24, 37, 37, 37, 37, 37, 37, 37, 37, 37, 24, 24, 24, 24, 24, 24, 24, 24, 2, 3, 3, 6, 6, 6, 6, 6, 24] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099053 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099053/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099053 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 89) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/89 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/89' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCc2ccc(NC(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)cc21) `ZINC001183099053.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183099053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099053/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001183099053 none CC(C)(C)OC(=O)N1CCCc2ccc(NC(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 34, 25, 34, 25, 25, 25, 25, 25, 25, 13, 2, 2, 1, 2, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 15, 25, 35, 35, 35, 35, 35, 35, 35, 35, 35, 25, 25, 25, 25, 25, 25, 25, 25, 2, 2, 2, 5, 5, 5, 5, 5, 25] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099053 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183099053 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099053/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099053/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099053 Building ZINC001183099053 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099053' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099053 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183099053 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099053/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099053 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 88) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/88: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCc2ccc(NC(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)cc21) `ZINC001183099053.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183099053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099053/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001183099053 none CC(C)(C)OC(=O)N1CCCc2ccc(NC(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 34, 24, 34, 24, 24, 24, 24, 24, 24, 13, 2, 2, 1, 2, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 16, 24, 37, 37, 37, 37, 37, 37, 37, 37, 37, 24, 24, 24, 24, 24, 24, 24, 24, 2, 3, 3, 6, 6, 6, 6, 6, 24] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099053 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099053/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099053 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 89) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/89: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCc2ccc(NC(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)cc21) `ZINC001183099053.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183099053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099053/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001183099053 none CC(C)(C)OC(=O)N1CCCc2ccc(NC(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 34, 25, 34, 25, 25, 25, 25, 25, 25, 13, 2, 2, 1, 2, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 15, 25, 35, 35, 35, 35, 35, 35, 35, 35, 35, 25, 25, 25, 25, 25, 25, 25, 25, 2, 2, 2, 5, 5, 5, 5, 5, 25] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099053 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183099053 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099053/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099053/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099053 Building ZINC001183099057 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099057' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099057 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183099057 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099057/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099057 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 90) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/90 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/90' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(C(F)(F)F)ccc1N1CCCCC1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183099057.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183099057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001183099057 none O=C(Nc1cc(C(F)(F)F)ccc1N1CCCCC1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 5, 5, 5, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 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: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 6, 6, 6, 6, 5, 6, 6, 10, 30, 30, 30, 30, 30, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 6, 6, 6, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 5, 5, 9, 9, 9, 9, 9] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099057 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099057/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099057 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 91) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/91 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/91' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(C(F)(F)F)ccc1N1CCCCC1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183099057.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183099057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099057/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001183099057 none O=C(Nc1cc(C(F)(F)F)ccc1N1CCCCC1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 5, 5, 5, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 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: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 11, 29, 29, 29, 29, 29, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 7, 7, 7, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 5, 5, 9, 9, 9, 9, 9] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099057 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183099057 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099057/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099057/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099057 Building ZINC001183099057 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099057' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099057 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183099057 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099057/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099057 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 90) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/90: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(C(F)(F)F)ccc1N1CCCCC1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183099057.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183099057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001183099057 none O=C(Nc1cc(C(F)(F)F)ccc1N1CCCCC1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 5, 5, 5, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 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: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 6, 6, 6, 6, 5, 6, 6, 10, 30, 30, 30, 30, 30, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 6, 6, 6, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 5, 5, 9, 9, 9, 9, 9] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099057 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099057/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099057 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 91) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/91: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(C(F)(F)F)ccc1N1CCCCC1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183099057.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183099057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099057/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001183099057 none O=C(Nc1cc(C(F)(F)F)ccc1N1CCCCC1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 5, 5, 5, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 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: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 11, 29, 29, 29, 29, 29, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 7, 7, 7, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 5, 5, 9, 9, 9, 9, 9] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099057 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183099057 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099057/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099057/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099057 Building ZINC001183099157 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001183099157 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 92) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/92 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/92' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc2c1[C@H]1Cc3ccccc3CN1CC2)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183099157.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183099157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001183099157 none O=C(Nc1cccc2c1[C@H]1Cc3ccccc3CN1CC2)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 5, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 9, 9, 20, 20, 20, 20, 20] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 74 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 93) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/93 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/93' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc2c1[C@H]1Cc3ccccc3CN1CC2)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183099157.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183099157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001183099157 none O=C(Nc1cccc2c1[C@H]1Cc3ccccc3CN1CC2)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 9, 9, 20, 20, 20, 20, 20] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 69 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 94) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/94 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/94' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc2c1[C@H]1Cc3ccccc3CN1CC2)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183099157.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001183099157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001183099157 none O=C(Nc1cccc2c1[C@H]1Cc3ccccc3CN1CC2)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 5, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 9, 9, 20, 20, 20, 20, 20] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 74 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 95) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/95 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/95' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc2c1[C@H]1Cc3ccccc3CN1CC2)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183099157.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001183099157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001183099157 none O=C(Nc1cccc2c1[C@H]1Cc3ccccc3CN1CC2)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 9, 9, 20, 20, 20, 20, 20] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 69 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183099157 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157 Building ZINC001183099157 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001183099157 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 92) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/92: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc2c1[C@H]1Cc3ccccc3CN1CC2)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183099157.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183099157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001183099157 none O=C(Nc1cccc2c1[C@H]1Cc3ccccc3CN1CC2)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 5, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 9, 9, 20, 20, 20, 20, 20] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 74 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 93) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/93: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc2c1[C@H]1Cc3ccccc3CN1CC2)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183099157.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183099157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001183099157 none O=C(Nc1cccc2c1[C@H]1Cc3ccccc3CN1CC2)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 9, 9, 20, 20, 20, 20, 20] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 69 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 94) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/94: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc2c1[C@H]1Cc3ccccc3CN1CC2)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183099157.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001183099157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001183099157 none O=C(Nc1cccc2c1[C@H]1Cc3ccccc3CN1CC2)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 5, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 9, 9, 20, 20, 20, 20, 20] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 74 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 95) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/95: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc2c1[C@H]1Cc3ccccc3CN1CC2)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183099157.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001183099157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001183099157 none O=C(Nc1cccc2c1[C@H]1Cc3ccccc3CN1CC2)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 9, 9, 20, 20, 20, 20, 20] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 69 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183099157 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157 Building ZINC001183099157 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001183099157 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 92) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/92: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc2c1[C@H]1Cc3ccccc3CN1CC2)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183099157.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183099157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001183099157 none O=C(Nc1cccc2c1[C@H]1Cc3ccccc3CN1CC2)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 5, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 9, 9, 20, 20, 20, 20, 20] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 74 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 93) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/93: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc2c1[C@H]1Cc3ccccc3CN1CC2)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183099157.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183099157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001183099157 none O=C(Nc1cccc2c1[C@H]1Cc3ccccc3CN1CC2)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 9, 9, 20, 20, 20, 20, 20] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 69 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 94) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/94: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc2c1[C@H]1Cc3ccccc3CN1CC2)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183099157.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001183099157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001183099157 none O=C(Nc1cccc2c1[C@H]1Cc3ccccc3CN1CC2)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 5, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 9, 9, 20, 20, 20, 20, 20] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 74 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 95) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/95: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc2c1[C@H]1Cc3ccccc3CN1CC2)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183099157.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001183099157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001183099157 none O=C(Nc1cccc2c1[C@H]1Cc3ccccc3CN1CC2)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 9, 9, 20, 20, 20, 20, 20] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 69 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183099157 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157 Building ZINC001183099157 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001183099157 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 92) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/92: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc2c1[C@H]1Cc3ccccc3CN1CC2)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183099157.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183099157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001183099157 none O=C(Nc1cccc2c1[C@H]1Cc3ccccc3CN1CC2)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 5, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 9, 9, 20, 20, 20, 20, 20] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 74 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 93) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/93: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc2c1[C@H]1Cc3ccccc3CN1CC2)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183099157.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183099157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001183099157 none O=C(Nc1cccc2c1[C@H]1Cc3ccccc3CN1CC2)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 9, 9, 20, 20, 20, 20, 20] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 69 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 94) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/94: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc2c1[C@H]1Cc3ccccc3CN1CC2)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183099157.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001183099157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001183099157 none O=C(Nc1cccc2c1[C@H]1Cc3ccccc3CN1CC2)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 5, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 9, 9, 20, 20, 20, 20, 20] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 74 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 95) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/95: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc2c1[C@H]1Cc3ccccc3CN1CC2)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183099157.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001183099157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001183099157 none O=C(Nc1cccc2c1[C@H]1Cc3ccccc3CN1CC2)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 9, 9, 20, 20, 20, 20, 20] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 69 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183099157 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099157 Building ZINC001183099158 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001183099158 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 96) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/96 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/96' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc2c1[C@@H]1Cc3ccccc3CN1CC2)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183099158.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183099158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001183099158 none O=C(Nc1cccc2c1[C@@H]1Cc3ccccc3CN1CC2)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 9, 9, 20, 20, 20, 20, 20] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 67 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 97) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/97 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/97' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc2c1[C@@H]1Cc3ccccc3CN1CC2)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183099158.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183099158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001183099158 none O=C(Nc1cccc2c1[C@@H]1Cc3ccccc3CN1CC2)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 9, 19, 19, 19, 19, 19] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 72 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 98) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/98 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/98' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc2c1[C@@H]1Cc3ccccc3CN1CC2)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183099158.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001183099158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001183099158 none O=C(Nc1cccc2c1[C@@H]1Cc3ccccc3CN1CC2)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 9, 9, 20, 20, 20, 20, 20] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 67 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 99) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/99 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/99' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc2c1[C@@H]1Cc3ccccc3CN1CC2)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183099158.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001183099158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001183099158 none O=C(Nc1cccc2c1[C@@H]1Cc3ccccc3CN1CC2)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 9, 19, 19, 19, 19, 19] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 72 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183099158 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158 Building ZINC001183099158 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001183099158 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 96) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/96: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc2c1[C@@H]1Cc3ccccc3CN1CC2)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183099158.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183099158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001183099158 none O=C(Nc1cccc2c1[C@@H]1Cc3ccccc3CN1CC2)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 9, 9, 20, 20, 20, 20, 20] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 67 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 97) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/97: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc2c1[C@@H]1Cc3ccccc3CN1CC2)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183099158.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183099158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001183099158 none O=C(Nc1cccc2c1[C@@H]1Cc3ccccc3CN1CC2)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 9, 19, 19, 19, 19, 19] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 72 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 98) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/98: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc2c1[C@@H]1Cc3ccccc3CN1CC2)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183099158.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001183099158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001183099158 none O=C(Nc1cccc2c1[C@@H]1Cc3ccccc3CN1CC2)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 9, 9, 20, 20, 20, 20, 20] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 67 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 99) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/99: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc2c1[C@@H]1Cc3ccccc3CN1CC2)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183099158.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001183099158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001183099158 none O=C(Nc1cccc2c1[C@@H]1Cc3ccccc3CN1CC2)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 9, 19, 19, 19, 19, 19] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 72 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183099158 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158 Building ZINC001183099158 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001183099158 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 96) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/96: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc2c1[C@@H]1Cc3ccccc3CN1CC2)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183099158.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183099158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001183099158 none O=C(Nc1cccc2c1[C@@H]1Cc3ccccc3CN1CC2)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 9, 9, 20, 20, 20, 20, 20] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 67 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 97) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/97: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc2c1[C@@H]1Cc3ccccc3CN1CC2)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183099158.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183099158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001183099158 none O=C(Nc1cccc2c1[C@@H]1Cc3ccccc3CN1CC2)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 9, 19, 19, 19, 19, 19] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 72 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 98) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/98: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc2c1[C@@H]1Cc3ccccc3CN1CC2)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183099158.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001183099158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001183099158 none O=C(Nc1cccc2c1[C@@H]1Cc3ccccc3CN1CC2)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 9, 9, 20, 20, 20, 20, 20] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 67 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 99) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/99: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc2c1[C@@H]1Cc3ccccc3CN1CC2)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183099158.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001183099158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001183099158 none O=C(Nc1cccc2c1[C@@H]1Cc3ccccc3CN1CC2)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 9, 19, 19, 19, 19, 19] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 72 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183099158 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158 Building ZINC001183099158 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001183099158 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 96) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/96: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc2c1[C@@H]1Cc3ccccc3CN1CC2)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183099158.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183099158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001183099158 none O=C(Nc1cccc2c1[C@@H]1Cc3ccccc3CN1CC2)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 9, 9, 20, 20, 20, 20, 20] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 67 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 97) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/97: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc2c1[C@@H]1Cc3ccccc3CN1CC2)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183099158.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183099158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001183099158 none O=C(Nc1cccc2c1[C@@H]1Cc3ccccc3CN1CC2)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 9, 19, 19, 19, 19, 19] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 72 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 98) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/98: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc2c1[C@@H]1Cc3ccccc3CN1CC2)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183099158.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001183099158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001183099158 none O=C(Nc1cccc2c1[C@@H]1Cc3ccccc3CN1CC2)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 9, 9, 20, 20, 20, 20, 20] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 67 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 99) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/99: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc2c1[C@@H]1Cc3ccccc3CN1CC2)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183099158.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001183099158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001183099158 none O=C(Nc1cccc2c1[C@@H]1Cc3ccccc3CN1CC2)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 9, 19, 19, 19, 19, 19] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 72 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183099158 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099158 Building ZINC001183099211 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099211' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099211 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183099211 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099211/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099211 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 100) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/100 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/100' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(N)ccc1CCc1ccc(NC(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)cc1C) `ZINC001183099211.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183099211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001183099211 none Cc1cc(N)ccc1CCc1ccc(NC(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 1, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 17, 17, 30, 30, 17, 17, 2, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 30, 30, 30, 30, 30, 30, 30, 30, 17, 17, 11, 11, 8, 8, 2, 2, 2, 3, 3, 3, 3, 3, 8, 8, 8, 8] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099211 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099211/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099211 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 101) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/101 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/101' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(N)ccc1CCc1ccc(NC(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)cc1C) `ZINC001183099211.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183099211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099211/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001183099211 none Cc1cc(N)ccc1CCc1ccc(NC(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 1, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 30, 17, 30, 30, 30, 17, 17, 4, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 30, 30, 30, 30, 30, 30, 30, 30, 17, 17, 17, 17, 8, 8, 2, 2, 2, 3, 3, 3, 3, 3, 8, 8, 8, 8] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099211 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183099211 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099211/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099211/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099211 Building ZINC001183099211 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099211' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099211 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183099211 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099211/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099211 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 100) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/100: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(N)ccc1CCc1ccc(NC(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)cc1C) `ZINC001183099211.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183099211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001183099211 none Cc1cc(N)ccc1CCc1ccc(NC(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 1, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 17, 17, 30, 30, 17, 17, 2, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 30, 30, 30, 30, 30, 30, 30, 30, 17, 17, 11, 11, 8, 8, 2, 2, 2, 3, 3, 3, 3, 3, 8, 8, 8, 8] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099211 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099211/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099211 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 101) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/101: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(N)ccc1CCc1ccc(NC(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)cc1C) `ZINC001183099211.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183099211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099211/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001183099211 none Cc1cc(N)ccc1CCc1ccc(NC(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 1, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 30, 17, 30, 30, 30, 17, 17, 4, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 30, 30, 30, 30, 30, 30, 30, 30, 17, 17, 17, 17, 8, 8, 2, 2, 2, 3, 3, 3, 3, 3, 8, 8, 8, 8] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099211 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183099211 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099211/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099211/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099211 Building ZINC001183099357 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099357' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099357 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183099357 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099357/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099357 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 102) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/102 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/102' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1(c2ccc(NC(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)cc2)CCC1) `ZINC001183099357.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183099357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001183099357 none CC(C)(C)OC(=O)NC1(c2ccc(NC(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)cc2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 27, 32, 27, 12, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 27, 27, 27, 32, 32, 32, 32, 32, 32, 32, 32, 32, 27, 6, 6, 2, 2, 2, 4, 4, 4, 4, 4, 6, 6, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099357 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099357/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099357 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 103) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/103 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/103' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1(c2ccc(NC(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)cc2)CCC1) `ZINC001183099357.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183099357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099357/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001183099357 none CC(C)(C)OC(=O)NC1(c2ccc(NC(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)cc2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 29, 32, 29, 13, 6, 7, 7, 2, 2, 1, 2, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 29, 29, 29, 32, 32, 32, 32, 32, 32, 32, 32, 32, 29, 7, 7, 2, 2, 2, 5, 5, 5, 5, 5, 7, 7, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099357 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183099357 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099357/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099357/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099357 Building ZINC001183099357 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099357' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099357 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183099357 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099357/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099357 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 102) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/102: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1(c2ccc(NC(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)cc2)CCC1) `ZINC001183099357.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183099357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001183099357 none CC(C)(C)OC(=O)NC1(c2ccc(NC(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)cc2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 27, 32, 27, 12, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 27, 27, 27, 32, 32, 32, 32, 32, 32, 32, 32, 32, 27, 6, 6, 2, 2, 2, 4, 4, 4, 4, 4, 6, 6, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099357 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099357/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099357 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 103) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/103: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1(c2ccc(NC(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)cc2)CCC1) `ZINC001183099357.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183099357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099357/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001183099357 none CC(C)(C)OC(=O)NC1(c2ccc(NC(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)cc2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 29, 32, 29, 13, 6, 7, 7, 2, 2, 1, 2, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 29, 29, 29, 32, 32, 32, 32, 32, 32, 32, 32, 32, 29, 7, 7, 2, 2, 2, 5, 5, 5, 5, 5, 7, 7, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099357 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183099357 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099357/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099357/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099357 Building ZINC001183099450 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099450' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099450 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183099450 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099450/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099450 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 104) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/104 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/104' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1cccc(Cl)c1NC(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183099450.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183099450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099450/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001183099450 none CC(C)(C)OC(=O)Nc1cccc(Cl)c1NC(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 18, 12, 18, 7, 7, 7, 5, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 30, 30, 30, 30, 30, 30, 30, 30, 30, 12, 7, 7, 7, 3, 3, 3, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099450 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099450/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099450 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 105) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/105 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/105' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1cccc(Cl)c1NC(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183099450.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183099450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099450/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001183099450 none CC(C)(C)OC(=O)Nc1cccc(Cl)c1NC(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 18, 11, 18, 7, 7, 7, 7, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 32, 32, 32, 32, 32, 32, 32, 32, 32, 11, 7, 7, 7, 3, 3, 3, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099450 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183099450 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099450/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099450/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099450 Building ZINC001183099450 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099450' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099450 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183099450 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099450/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099450 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 104) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/104: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1cccc(Cl)c1NC(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183099450.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183099450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099450/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001183099450 none CC(C)(C)OC(=O)Nc1cccc(Cl)c1NC(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 18, 12, 18, 7, 7, 7, 5, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 30, 30, 30, 30, 30, 30, 30, 30, 30, 12, 7, 7, 7, 3, 3, 3, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099450 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099450/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099450 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 105) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/105: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1cccc(Cl)c1NC(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183099450.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183099450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099450/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001183099450 none CC(C)(C)OC(=O)Nc1cccc(Cl)c1NC(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 18, 11, 18, 7, 7, 7, 7, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 32, 32, 32, 32, 32, 32, 32, 32, 32, 11, 7, 7, 7, 3, 3, 3, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099450 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183099450 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099450/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099450/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099450 Building ZINC001183099451 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099451' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099451 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183099451 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099451/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099451 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 106) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/106 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/106' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@@H](c2ccc(NC(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)cc2)C1) `ZINC001183099451.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183099451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099451/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001183099451 none CC(C)(C)OC(=O)N1CC[C@@H](c2ccc(NC(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 20, 31, 20, 20, 20, 10, 20, 4, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 20, 31, 31, 31, 31, 31, 31, 31, 31, 31, 20, 20, 20, 20, 6, 6, 2, 2, 2, 3, 3, 3, 3, 3, 6, 6, 20, 20] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099451 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099451/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099451 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 107) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/107 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/107' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@@H](c2ccc(NC(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)cc2)C1) `ZINC001183099451.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183099451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099451/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001183099451 none CC(C)(C)OC(=O)N1CC[C@@H](c2ccc(NC(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 20, 31, 20, 20, 20, 3, 20, 2, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 20, 31, 31, 31, 31, 31, 31, 31, 31, 31, 20, 20, 20, 20, 6, 6, 2, 2, 2, 3, 3, 3, 3, 3, 6, 6, 20, 20] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099451 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183099451 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099451/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099451/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099451 Building ZINC001183099451 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099451' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099451 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183099451 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099451/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099451 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 106) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/106: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@@H](c2ccc(NC(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)cc2)C1) `ZINC001183099451.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183099451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099451/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001183099451 none CC(C)(C)OC(=O)N1CC[C@@H](c2ccc(NC(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 20, 31, 20, 20, 20, 10, 20, 4, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 20, 31, 31, 31, 31, 31, 31, 31, 31, 31, 20, 20, 20, 20, 6, 6, 2, 2, 2, 3, 3, 3, 3, 3, 6, 6, 20, 20] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099451 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099451/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099451 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 107) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/107: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@@H](c2ccc(NC(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)cc2)C1) `ZINC001183099451.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183099451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099451/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001183099451 none CC(C)(C)OC(=O)N1CC[C@@H](c2ccc(NC(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 20, 31, 20, 20, 20, 3, 20, 2, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 20, 31, 31, 31, 31, 31, 31, 31, 31, 31, 20, 20, 20, 20, 6, 6, 2, 2, 2, 3, 3, 3, 3, 3, 6, 6, 20, 20] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099451 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183099451 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099451/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099451/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099451 Building ZINC001183099459 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099459' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099459 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183099459 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099459/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099459 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 108) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/108 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/108' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@H](c2ccc(NC(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)cc2)C1) `ZINC001183099459.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183099459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099459/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001183099459 none CC(C)(C)OC(=O)N1CC[C@H](c2ccc(NC(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 20, 32, 20, 20, 20, 3, 20, 2, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 20, 32, 32, 32, 32, 32, 32, 32, 32, 32, 20, 20, 20, 20, 6, 6, 2, 2, 2, 3, 3, 3, 3, 3, 6, 6, 20, 20] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099459 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099459/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099459 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 109) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/109 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/109' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@H](c2ccc(NC(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)cc2)C1) `ZINC001183099459.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183099459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099459/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001183099459 none CC(C)(C)OC(=O)N1CC[C@H](c2ccc(NC(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 18, 28, 18, 18, 18, 3, 18, 2, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 18, 28, 28, 28, 28, 28, 28, 28, 28, 28, 18, 18, 18, 18, 6, 6, 2, 2, 2, 3, 3, 3, 3, 3, 6, 6, 18, 18] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099459 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183099459 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099459/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099459/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099459 Building ZINC001183099459 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099459' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099459 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183099459 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099459/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099459 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 108) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/108: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@H](c2ccc(NC(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)cc2)C1) `ZINC001183099459.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183099459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099459/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001183099459 none CC(C)(C)OC(=O)N1CC[C@H](c2ccc(NC(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 20, 32, 20, 20, 20, 3, 20, 2, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 20, 32, 32, 32, 32, 32, 32, 32, 32, 32, 20, 20, 20, 20, 6, 6, 2, 2, 2, 3, 3, 3, 3, 3, 6, 6, 20, 20] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099459 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099459/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099459 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 109) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/109: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@H](c2ccc(NC(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)cc2)C1) `ZINC001183099459.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183099459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099459/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001183099459 none CC(C)(C)OC(=O)N1CC[C@H](c2ccc(NC(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 18, 28, 18, 18, 18, 3, 18, 2, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 18, 28, 28, 28, 28, 28, 28, 28, 28, 28, 18, 18, 18, 18, 6, 6, 2, 2, 2, 3, 3, 3, 3, 3, 6, 6, 18, 18] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099459 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183099459 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099459/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099459/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099459 Building ZINC001183099471 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099471' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099471 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183099471 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099471/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099471 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 110) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/110 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/110' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1C1(NC(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CCC(F)(F)CC1) `ZINC001183099471.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183099471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099471/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001183099471 none COc1ccccc1C1(NC(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CCC(F)(F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 7, 5, 1, 5, 1, 1, 1, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 21, 21, 21, 21, 21, 21, 21, 26, 26, 26, 26, 26, 26, 26, 5, 7, 7, 16, 16, 16, 16, 16, 21, 21, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 92 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099471 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099471/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099471 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 111) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/111 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/111' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1C1(NC(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CCC(F)(F)CC1) `ZINC001183099471.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183099471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099471/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001183099471 none COc1ccccc1C1(NC(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CCC(F)(F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 17, 6, 4, 1, 4, 1, 1, 1, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 17, 17, 17, 17, 17, 17, 17, 23, 23, 23, 23, 23, 23, 23, 4, 6, 6, 14, 14, 14, 14, 14, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 83 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099471 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183099471 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099471/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099471/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099471 Building ZINC001183099471 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099471' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099471 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183099471 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099471/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099471 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 110) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/110: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1C1(NC(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CCC(F)(F)CC1) `ZINC001183099471.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183099471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099471/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001183099471 none COc1ccccc1C1(NC(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CCC(F)(F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 7, 5, 1, 5, 1, 1, 1, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 21, 21, 21, 21, 21, 21, 21, 26, 26, 26, 26, 26, 26, 26, 5, 7, 7, 16, 16, 16, 16, 16, 21, 21, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 92 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099471 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099471/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099471 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 111) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/111: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1C1(NC(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CCC(F)(F)CC1) `ZINC001183099471.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183099471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099471/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001183099471 none COc1ccccc1C1(NC(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CCC(F)(F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 17, 6, 4, 1, 4, 1, 1, 1, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 17, 17, 17, 17, 17, 17, 17, 23, 23, 23, 23, 23, 23, 23, 4, 6, 6, 14, 14, 14, 14, 14, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 83 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099471 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183099471 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099471/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099471/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099471 Building ZINC001183099548 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099548' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099548 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183099548 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099548/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099548 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 112) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/112 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/112' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(F)cc1)c1ccc(Cl)c(NC(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)c1) `ZINC001183099548.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183099548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001183099548 none O=C(Nc1ccc(F)cc1)c1ccc(Cl)c(NC(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 18, 19, 20, 20, 8, 8, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 8, 14, 20, 20, 20, 20, 8, 8, 3, 5, 5, 9, 9, 9, 9, 9, 8] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099548 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099548/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099548 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 113) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/113 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/113' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(F)cc1)c1ccc(Cl)c(NC(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)c1) `ZINC001183099548.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183099548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099548/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001183099548 none O=C(Nc1ccc(F)cc1)c1ccc(Cl)c(NC(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 24, 14, 14, 24, 24, 8, 8, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 8, 14, 24, 24, 24, 24, 8, 8, 3, 5, 5, 9, 9, 9, 9, 9, 8] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099548 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183099548 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099548/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099548/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099548 Building ZINC001183099548 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099548' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099548 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183099548 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099548/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099548 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 112) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/112: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(F)cc1)c1ccc(Cl)c(NC(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)c1) `ZINC001183099548.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183099548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001183099548 none O=C(Nc1ccc(F)cc1)c1ccc(Cl)c(NC(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 18, 19, 20, 20, 8, 8, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 8, 14, 20, 20, 20, 20, 8, 8, 3, 5, 5, 9, 9, 9, 9, 9, 8] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099548 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099548/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099548 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 113) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/113: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(F)cc1)c1ccc(Cl)c(NC(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)c1) `ZINC001183099548.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183099548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099548/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001183099548 none O=C(Nc1ccc(F)cc1)c1ccc(Cl)c(NC(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 24, 14, 14, 24, 24, 8, 8, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 8, 14, 24, 24, 24, 24, 8, 8, 3, 5, 5, 9, 9, 9, 9, 9, 8] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099548 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183099548 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099548/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099548/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099548 Building ZINC001183099554 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099554' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099554 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183099554 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099554/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099554 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 114) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/114 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/114' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(OC(F)(F)F)c(C(F)(F)F)c1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183099554.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183099554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001183099554 none O=C(Nc1ccc(OC(F)(F)F)c(C(F)(F)F)c1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 15, 15, 15, 1, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 11, 11, 8, 10, 26, 35, 35, 35, 11, 11, 11, 11, 11, 11, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 11, 11, 11, 2, 2, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099554 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099554/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099554 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 115) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/115 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/115' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(OC(F)(F)F)c(C(F)(F)F)c1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183099554.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183099554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099554/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001183099554 none O=C(Nc1ccc(OC(F)(F)F)c(C(F)(F)F)c1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 15, 15, 15, 1, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 11, 11, 2, 8, 26, 35, 35, 35, 11, 11, 11, 11, 11, 11, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 11, 11, 11, 2, 2, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099554 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183099554 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099554/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099554/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099554 Building ZINC001183099554 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099554' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099554 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183099554 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099554/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099554 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 114) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/114: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(OC(F)(F)F)c(C(F)(F)F)c1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183099554.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183099554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001183099554 none O=C(Nc1ccc(OC(F)(F)F)c(C(F)(F)F)c1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 15, 15, 15, 1, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 11, 11, 8, 10, 26, 35, 35, 35, 11, 11, 11, 11, 11, 11, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 11, 11, 11, 2, 2, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099554 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099554/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099554 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 115) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/115: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(OC(F)(F)F)c(C(F)(F)F)c1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183099554.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183099554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099554/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001183099554 none O=C(Nc1ccc(OC(F)(F)F)c(C(F)(F)F)c1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 15, 15, 15, 1, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 11, 11, 2, 8, 26, 35, 35, 35, 11, 11, 11, 11, 11, 11, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 11, 11, 11, 2, 2, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099554 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183099554 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099554/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099554/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183099554 Building ZINC001183100856 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183100856' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183100856 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183100856 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183100856/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183100856 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 116) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/116 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/116' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1c2ccccc2nc1[C@H](NC(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12)c1ccccc1) `ZINC001183100856.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183100856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183100856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001183100856 none CCn1c2ccccc2nc1[C@H](NC(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 7, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 3, 6, 3, 1, 3, 1, 1, 1, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 13, 13, 6, 13, 13, 23, 23, 23, 23, 23, 19, 19, 19, 19, 3, 7, 7, 12, 12, 12, 12, 12, 13, 13, 6, 13, 13] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 130 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183100856 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183100856/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183100856 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 117) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/117 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/117' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1c2ccccc2nc1[C@H](NC(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12)c1ccccc1) `ZINC001183100856.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183100856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183100856/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001183100856 none CCn1c2ccccc2nc1[C@H](NC(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 7, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 3, 6, 3, 1, 3, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 11, 11, 6, 11, 11, 21, 21, 21, 21, 21, 16, 16, 16, 16, 3, 7, 7, 15, 15, 15, 15, 15, 11, 11, 6, 11, 11] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 125 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183100856 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183100856 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183100856/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183100856/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183100856 Building ZINC001183100856 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183100856' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183100856 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183100856 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183100856/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183100856 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 116) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/116: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1c2ccccc2nc1[C@H](NC(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12)c1ccccc1) `ZINC001183100856.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183100856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183100856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001183100856 none CCn1c2ccccc2nc1[C@H](NC(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 7, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 3, 6, 3, 1, 3, 1, 1, 1, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 13, 13, 6, 13, 13, 23, 23, 23, 23, 23, 19, 19, 19, 19, 3, 7, 7, 12, 12, 12, 12, 12, 13, 13, 6, 13, 13] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 130 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183100856 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183100856/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183100856 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 117) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/117: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1c2ccccc2nc1[C@H](NC(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12)c1ccccc1) `ZINC001183100856.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183100856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183100856/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001183100856 none CCn1c2ccccc2nc1[C@H](NC(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 7, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 3, 6, 3, 1, 3, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 11, 11, 6, 11, 11, 21, 21, 21, 21, 21, 16, 16, 16, 16, 3, 7, 7, 15, 15, 15, 15, 15, 11, 11, 6, 11, 11] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 125 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183100856 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183100856 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183100856/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183100856/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183100856 Building ZINC001183100857 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183100857' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183100857 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183100857 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183100857/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183100857 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 118) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/118 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/118' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1c2ccccc2nc1[C@@H](NC(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12)c1ccccc1) `ZINC001183100857.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183100857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183100857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001183100857 none CCn1c2ccccc2nc1[C@@H](NC(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 7, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 3, 6, 3, 1, 3, 1, 1, 1, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 11, 11, 6, 11, 11, 21, 21, 21, 21, 21, 16, 16, 16, 16, 3, 6, 6, 14, 14, 14, 14, 14, 11, 11, 6, 11, 11] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 122 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183100857 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183100857/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183100857 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 119) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/119 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/119' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1c2ccccc2nc1[C@@H](NC(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12)c1ccccc1) `ZINC001183100857.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183100857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183100857/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001183100857 none CCn1c2ccccc2nc1[C@@H](NC(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 7, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 3, 6, 3, 1, 3, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 13, 13, 6, 13, 13, 23, 23, 23, 23, 23, 19, 19, 19, 19, 3, 7, 7, 11, 11, 11, 11, 11, 13, 13, 6, 13, 13] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 128 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183100857 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183100857 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183100857/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183100857/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183100857 Building ZINC001183100857 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183100857' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183100857 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183100857 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183100857/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183100857 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 118) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/118: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1c2ccccc2nc1[C@@H](NC(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12)c1ccccc1) `ZINC001183100857.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183100857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183100857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001183100857 none CCn1c2ccccc2nc1[C@@H](NC(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 7, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 3, 6, 3, 1, 3, 1, 1, 1, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 11, 11, 6, 11, 11, 21, 21, 21, 21, 21, 16, 16, 16, 16, 3, 6, 6, 14, 14, 14, 14, 14, 11, 11, 6, 11, 11] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 122 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183100857 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183100857/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183100857 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 119) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/119: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1c2ccccc2nc1[C@@H](NC(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12)c1ccccc1) `ZINC001183100857.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183100857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183100857/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001183100857 none CCn1c2ccccc2nc1[C@@H](NC(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 7, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 3, 6, 3, 1, 3, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 13, 13, 6, 13, 13, 23, 23, 23, 23, 23, 19, 19, 19, 19, 3, 7, 7, 11, 11, 11, 11, 11, 13, 13, 6, 13, 13] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 128 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183100857 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183100857 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183100857/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183100857/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183100857 Building ZINC001183136771 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183136771' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183136771 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183136771 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183136771/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183136771 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 120) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/120 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/120' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC=C(C(C)(C)C)CC1) `ZINC001183136771.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183136771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183136771/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001183136771 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC=C(C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.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, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 23, 23, 4, 23, 23, 23, 23, 23, 23, 3, 3, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 9, 9, 9, 4, 4, 3, 3, 3, 23, 23, 6, 23, 3, 3, 3, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 88 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183136771 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183136771/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183136771 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 121) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/121 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/121' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC=C(C(C)(C)C)CC1) `ZINC001183136771.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183136771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183136771/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001183136771 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC=C(C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.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, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 20, 20, 2, 20, 20, 20, 20, 20, 20, 2, 2, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 8, 8, 8, 4, 4, 2, 2, 2, 20, 20, 2, 20, 2, 2, 2, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 72 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183136771 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183136771 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183136771/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183136771/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183136771 Building ZINC001183136771 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183136771' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183136771 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183136771 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183136771/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183136771 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 120) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/120: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC=C(C(C)(C)C)CC1) `ZINC001183136771.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183136771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183136771/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001183136771 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC=C(C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.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, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 23, 23, 4, 23, 23, 23, 23, 23, 23, 3, 3, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 9, 9, 9, 4, 4, 3, 3, 3, 23, 23, 6, 23, 3, 3, 3, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 88 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183136771 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183136771/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183136771 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 121) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/121: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC=C(C(C)(C)C)CC1) `ZINC001183136771.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183136771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183136771/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001183136771 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC=C(C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.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, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 20, 20, 2, 20, 20, 20, 20, 20, 20, 2, 2, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 8, 8, 8, 4, 4, 2, 2, 2, 20, 20, 2, 20, 2, 2, 2, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 72 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183136771 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183136771 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183136771/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183136771/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183136771 Building ZINC001183364349 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183364349' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183364349 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183364349 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183364349/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183364349 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 122) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/122 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/122' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(C(=O)Nc3ccc(F)cc3)ccc2Cl)cc1) `ZINC001183364349.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183364349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183364349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001183364349 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(C(=O)Nc3ccc(F)cc3)ccc2Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 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: [6, 1, 1, 6, 6, 1, 1, 1, 1, 5, 5, 5, 11, 11, 11, 20, 20, 20, 44, 44, 20, 20, 44, 44, 11, 11, 11, 11, 6, 6, 6, 6, 6, 6, 6, 5, 11, 20, 44, 44, 44, 44, 11, 11, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183364349 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183364349/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183364349 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 123) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/123 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/123' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(C(=O)Nc3ccc(F)cc3)ccc2Cl)cc1) `ZINC001183364349.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183364349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183364349/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001183364349 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(C(=O)Nc3ccc(F)cc3)ccc2Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 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: [6, 1, 1, 6, 6, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 19, 19, 19, 44, 44, 19, 19, 44, 44, 10, 10, 10, 10, 6, 6, 6, 6, 6, 6, 6, 4, 10, 19, 44, 44, 44, 44, 10, 10, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183364349 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183364349 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183364349/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183364349/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183364349 Building ZINC001183364349 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183364349' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183364349 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183364349 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183364349/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183364349 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 122) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/122: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(C(=O)Nc3ccc(F)cc3)ccc2Cl)cc1) `ZINC001183364349.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183364349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183364349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001183364349 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(C(=O)Nc3ccc(F)cc3)ccc2Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 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: [6, 1, 1, 6, 6, 1, 1, 1, 1, 5, 5, 5, 11, 11, 11, 20, 20, 20, 44, 44, 20, 20, 44, 44, 11, 11, 11, 11, 6, 6, 6, 6, 6, 6, 6, 5, 11, 20, 44, 44, 44, 44, 11, 11, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183364349 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183364349/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183364349 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 123) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/123: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(C(=O)Nc3ccc(F)cc3)ccc2Cl)cc1) `ZINC001183364349.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183364349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183364349/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001183364349 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(C(=O)Nc3ccc(F)cc3)ccc2Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 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: [6, 1, 1, 6, 6, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 19, 19, 19, 44, 44, 19, 19, 44, 44, 10, 10, 10, 10, 6, 6, 6, 6, 6, 6, 6, 4, 10, 19, 44, 44, 44, 44, 10, 10, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183364349 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183364349 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183364349/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183364349/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183364349 Building ZINC001183366335 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183366335' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183366335 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183366335 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183366335/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183366335 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 124) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/124 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/124' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(c3ccc(NC(=O)OC(C)(C)C)cc3)CC2)cc1) `ZINC001183366335.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183366335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183366335/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001183366335 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(c3ccc(NC(=O)OC(C)(C)C)cc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 6, 6, 4, 6, 24, 43, 43, 50, 50, 50, 50, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183366335 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183366335/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183366335 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 125) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/125 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/125' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(c3ccc(NC(=O)OC(C)(C)C)cc3)CC2)cc1) `ZINC001183366335.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183366335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183366335/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001183366335 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(c3ccc(NC(=O)OC(C)(C)C)cc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 8, 8, 4, 8, 28, 42, 42, 50, 50, 50, 50, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 8, 8, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183366335 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183366335 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183366335/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183366335/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183366335 Building ZINC001183366335 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183366335' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183366335 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183366335 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183366335/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183366335 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 124) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/124: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(c3ccc(NC(=O)OC(C)(C)C)cc3)CC2)cc1) `ZINC001183366335.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183366335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183366335/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001183366335 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(c3ccc(NC(=O)OC(C)(C)C)cc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 6, 6, 4, 6, 24, 43, 43, 50, 50, 50, 50, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183366335 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183366335/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183366335 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 125) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/125: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(c3ccc(NC(=O)OC(C)(C)C)cc3)CC2)cc1) `ZINC001183366335.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183366335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183366335/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001183366335 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(c3ccc(NC(=O)OC(C)(C)C)cc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 8, 8, 4, 8, 28, 42, 42, 50, 50, 50, 50, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 8, 8, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183366335 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183366335 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183366335/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183366335/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183366335 Building ZINC001183367022 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183367022' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183367022 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183367022 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183367022/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183367022 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 126) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/126 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/126' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(C(=O)c3ccc(c4ccccc4)cc3)CC2)cc1) `ZINC001183367022.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183367022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183367022/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001183367022 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(C(=O)c3ccc(c4ccccc4)cc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 20, 20, 29, 29, 20, 27, 50, 50, 44, 50, 50, 29, 29, 4, 4, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 29, 29, 50, 50, 46, 50, 50, 29, 29, 4, 4, 4, 4, 2, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183367022 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183367022/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183367022 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 127) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/127 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/127' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(C(=O)c3ccc(c4ccccc4)cc3)CC2)cc1) `ZINC001183367022.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183367022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183367022/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001183367022 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(C(=O)c3ccc(c4ccccc4)cc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 20, 20, 33, 33, 24, 28, 50, 50, 28, 50, 50, 33, 33, 4, 4, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 33, 33, 50, 50, 45, 50, 50, 33, 33, 4, 4, 4, 4, 2, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183367022 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183367022 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183367022/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183367022/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183367022 Building ZINC001183367022 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183367022' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183367022 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183367022 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183367022/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183367022 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 126) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/126: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(C(=O)c3ccc(c4ccccc4)cc3)CC2)cc1) `ZINC001183367022.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183367022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183367022/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001183367022 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(C(=O)c3ccc(c4ccccc4)cc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 20, 20, 29, 29, 20, 27, 50, 50, 44, 50, 50, 29, 29, 4, 4, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 29, 29, 50, 50, 46, 50, 50, 29, 29, 4, 4, 4, 4, 2, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183367022 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183367022/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183367022 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 127) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/127: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(C(=O)c3ccc(c4ccccc4)cc3)CC2)cc1) `ZINC001183367022.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183367022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183367022/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001183367022 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(C(=O)c3ccc(c4ccccc4)cc3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 20, 20, 33, 33, 24, 28, 50, 50, 28, 50, 50, 33, 33, 4, 4, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 33, 33, 50, 50, 45, 50, 50, 33, 33, 4, 4, 4, 4, 2, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183367022 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183367022 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183367022/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183367022/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183367022 Building ZINC001183451665 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183451665' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183451665 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183451665 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183451665/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183451665 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 128) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/128 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/128' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(c3cccc(OCc4ccccc4Cl)c3)CC2)cc1) `ZINC001183451665.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183451665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183451665/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001183451665 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(c3cccc(OCc4ccccc4Cl)c3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 16, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 17, 17, 17, 17, 17, 27, 27, 50, 50, 50, 50, 50, 50, 17, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 17, 17, 17, 27, 27, 50, 50, 50, 50, 17, 4, 4, 4, 4, 1, 1] 50 rigid atoms, others: [0, 1, 34, 3, 32, 5, 6, 33, 7, 2, 35, 55, 56, 4, 36, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183451665 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183451665/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183451665 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 129) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/129 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/129' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(c3cccc(OCc4ccccc4Cl)c3)CC2)cc1) `ZINC001183451665.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183451665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183451665/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001183451665 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(c3cccc(OCc4ccccc4Cl)c3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 16, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 18, 18, 18, 18, 18, 28, 28, 50, 50, 50, 50, 50, 50, 18, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 18, 18, 18, 28, 28, 50, 50, 50, 50, 18, 4, 4, 4, 4, 1, 1] 50 rigid atoms, others: [0, 1, 34, 3, 32, 5, 6, 33, 7, 2, 35, 55, 56, 4, 36, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183451665 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183451665 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183451665/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183451665/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183451665 Building ZINC001183451665 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183451665' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183451665 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183451665 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183451665/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183451665 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 128) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/128: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(c3cccc(OCc4ccccc4Cl)c3)CC2)cc1) `ZINC001183451665.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183451665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183451665/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001183451665 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(c3cccc(OCc4ccccc4Cl)c3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 16, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 17, 17, 17, 17, 17, 27, 27, 50, 50, 50, 50, 50, 50, 17, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 17, 17, 17, 27, 27, 50, 50, 50, 50, 17, 4, 4, 4, 4, 1, 1] 50 rigid atoms, others: [0, 1, 34, 3, 32, 5, 6, 33, 7, 2, 35, 55, 56, 4, 36, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183451665 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183451665/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183451665 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 129) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/129: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(c3cccc(OCc4ccccc4Cl)c3)CC2)cc1) `ZINC001183451665.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183451665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183451665/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001183451665 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(c3cccc(OCc4ccccc4Cl)c3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 16, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 18, 18, 18, 18, 18, 28, 28, 50, 50, 50, 50, 50, 50, 18, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 18, 18, 18, 28, 28, 50, 50, 50, 50, 18, 4, 4, 4, 4, 1, 1] 50 rigid atoms, others: [0, 1, 34, 3, 32, 5, 6, 33, 7, 2, 35, 55, 56, 4, 36, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183451665 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183451665 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183451665/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183451665/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183451665 Building ZINC001183755845 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183755845' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183755845 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183755845 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183755845/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183755845 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 130) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/130 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/130' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]1c1ccc(C)cc1) `ZINC001183755845.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183755845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183755845/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001183755845 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]1c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 21, 21, 4, 21, 21, 21, 21, 21, 21, 4, 4, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 11, 11, 8, 8, 11, 11, 4, 4, 4, 21, 21, 4, 21, 4, 4, 4, 3, 8, 8, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 104 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183755845 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183755845/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183755845 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 131) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/131 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/131' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]1c1ccc(C)cc1) `ZINC001183755845.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183755845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183755845/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001183755845 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]1c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 17, 17, 3, 17, 17, 17, 17, 17, 17, 3, 3, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 13, 13, 9, 10, 13, 13, 3, 3, 3, 17, 17, 3, 17, 3, 3, 3, 2, 8, 8, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 100 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183755845 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183755845 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183755845/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183755845/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183755845 Building ZINC001183755845 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183755845' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183755845 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183755845 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183755845/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183755845 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 130) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/130: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]1c1ccc(C)cc1) `ZINC001183755845.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183755845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183755845/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001183755845 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]1c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 21, 21, 4, 21, 21, 21, 21, 21, 21, 4, 4, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 11, 11, 8, 8, 11, 11, 4, 4, 4, 21, 21, 4, 21, 4, 4, 4, 3, 8, 8, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 104 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183755845 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183755845/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183755845 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 131) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/131: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]1c1ccc(C)cc1) `ZINC001183755845.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183755845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183755845/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001183755845 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]1c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 17, 17, 3, 17, 17, 17, 17, 17, 17, 3, 3, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 13, 13, 9, 10, 13, 13, 3, 3, 3, 17, 17, 3, 17, 3, 3, 3, 2, 8, 8, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 100 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183755845 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183755845 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183755845/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183755845/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183755845 Building ZINC001183933306 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183933306' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183933306 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183933306 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183933306/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183933306 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 132) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/132 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/132' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2ccc(C)cc2C1) `ZINC001183933306.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183933306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183933306/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001183933306 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2ccc(C)cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 18, 18, 3, 18, 18, 18, 18, 18, 18, 3, 3, 1, 1, 1, 2, 4, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 18, 18, 3, 18, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 58 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183933306 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183933306/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183933306 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 133) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/133 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/133' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2ccc(C)cc2C1) `ZINC001183933306.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183933306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183933306/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001183933306 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2ccc(C)cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 18, 18, 3, 18, 18, 18, 18, 18, 18, 3, 3, 1, 1, 1, 2, 4, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 18, 18, 3, 18, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 58 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183933306 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183933306 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183933306/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183933306/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183933306 Building ZINC001183933306 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183933306' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183933306 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183933306 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183933306/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183933306 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 132) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/132: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2ccc(C)cc2C1) `ZINC001183933306.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183933306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183933306/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001183933306 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2ccc(C)cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 18, 18, 3, 18, 18, 18, 18, 18, 18, 3, 3, 1, 1, 1, 2, 4, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 18, 18, 3, 18, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 58 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183933306 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183933306/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183933306 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 133) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/133: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2ccc(C)cc2C1) `ZINC001183933306.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183933306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183933306/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001183933306 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2ccc(C)cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 18, 18, 3, 18, 18, 18, 18, 18, 18, 3, 3, 1, 1, 1, 2, 4, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 18, 18, 3, 18, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 58 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183933306 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001183933306 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183933306/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183933306/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001183933306 Building ZINC001184248167 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184248167' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184248167 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184248167 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184248167/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184248167 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 134) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/134 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/134' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2ccc(Oc3ccc(C(C)(C)C)cc3)nc2)ccc1O) `ZINC001184248167.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184248167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184248167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184248167 none COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2ccc(Oc3ccc(C(C)(C)C)cc3)nc2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 8, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [5, 3, 3, 3, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 18, 18, 18, 18, 18, 31, 31, 31, 18, 18, 3, 3, 3, 3, 3, 3, 5, 5, 5, 3, 2, 2, 1, 3, 3, 18, 18, 31, 31, 31, 31, 31, 31, 31, 31, 31, 18, 18, 3, 3, 3, 6] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 38] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184248167 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184248167/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184248167 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 135) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/135 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/135' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2ccc(Oc3ccc(C(C)(C)C)cc3)nc2)ccc1O) `ZINC001184248167.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184248167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184248167/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184248167 none COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2ccc(Oc3ccc(C(C)(C)C)cc3)nc2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 8, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [5, 3, 3, 3, 2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 19, 19, 19, 19, 19, 31, 31, 31, 19, 19, 4, 4, 3, 3, 3, 3, 5, 5, 5, 3, 2, 2, 1, 4, 4, 19, 19, 31, 31, 31, 31, 31, 31, 31, 31, 31, 19, 19, 4, 3, 3, 6] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 38] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184248167 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184248167 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184248167/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184248167/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184248167 Building ZINC001184248167 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184248167' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184248167 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184248167 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184248167/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184248167 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 134) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/134: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2ccc(Oc3ccc(C(C)(C)C)cc3)nc2)ccc1O) `ZINC001184248167.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184248167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184248167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184248167 none COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2ccc(Oc3ccc(C(C)(C)C)cc3)nc2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 8, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [5, 3, 3, 3, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 18, 18, 18, 18, 18, 31, 31, 31, 18, 18, 3, 3, 3, 3, 3, 3, 5, 5, 5, 3, 2, 2, 1, 3, 3, 18, 18, 31, 31, 31, 31, 31, 31, 31, 31, 31, 18, 18, 3, 3, 3, 6] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 38] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184248167 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184248167/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184248167 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 135) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/135: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2ccc(Oc3ccc(C(C)(C)C)cc3)nc2)ccc1O) `ZINC001184248167.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184248167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184248167/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184248167 none COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2ccc(Oc3ccc(C(C)(C)C)cc3)nc2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 8, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [5, 3, 3, 3, 2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 19, 19, 19, 19, 19, 31, 31, 31, 19, 19, 4, 4, 3, 3, 3, 3, 5, 5, 5, 3, 2, 2, 1, 4, 4, 19, 19, 31, 31, 31, 31, 31, 31, 31, 31, 31, 19, 19, 4, 3, 3, 6] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 38] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184248167 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184248167 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184248167/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184248167/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184248167 Building ZINC001184248989 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184248989' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184248989 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184248989 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184248989/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184248989 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 136) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/136 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/136' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2csc(C(F)(F)F)c2c2ccccc2)ccc1O) `ZINC001184248989.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184248989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184248989/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001184248989 none COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2csc(C(F)(F)F)c2c2ccccc2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 1, 14, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [20, 11, 11, 11, 6, 1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 16, 16, 11, 16, 16, 11, 11, 11, 11, 20, 20, 20, 11, 6, 6, 3, 11, 16, 16, 13, 16, 16, 11, 11, 22] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184248989 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184248989/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184248989 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 137) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/137 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/137' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2csc(C(F)(F)F)c2c2ccccc2)ccc1O) `ZINC001184248989.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184248989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184248989/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001184248989 none COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2csc(C(F)(F)F)c2c2ccccc2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 1, 14, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [20, 11, 11, 11, 6, 1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 17, 17, 11, 17, 17, 11, 11, 11, 11, 20, 20, 20, 11, 6, 6, 3, 11, 17, 17, 12, 17, 17, 11, 11, 22] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184248989 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184248989 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184248989/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184248989/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184248989 Building ZINC001184248989 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184248989' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184248989 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184248989 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184248989/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184248989 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 136) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/136: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2csc(C(F)(F)F)c2c2ccccc2)ccc1O) `ZINC001184248989.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184248989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184248989/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001184248989 none COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2csc(C(F)(F)F)c2c2ccccc2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 1, 14, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [20, 11, 11, 11, 6, 1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 16, 16, 11, 16, 16, 11, 11, 11, 11, 20, 20, 20, 11, 6, 6, 3, 11, 16, 16, 13, 16, 16, 11, 11, 22] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184248989 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184248989/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184248989 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 137) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/137: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2csc(C(F)(F)F)c2c2ccccc2)ccc1O) `ZINC001184248989.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184248989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184248989/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001184248989 none COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2csc(C(F)(F)F)c2c2ccccc2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 1, 14, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [20, 11, 11, 11, 6, 1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 17, 17, 11, 17, 17, 11, 11, 11, 11, 20, 20, 20, 11, 6, 6, 3, 11, 17, 17, 12, 17, 17, 11, 11, 22] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184248989 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184248989 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184248989/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184248989/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184248989 Building ZINC001184251740 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184251740' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184251740 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184251740 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184251740/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184251740 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 138) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/138 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/138' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2ccc(c3ccc(N)cc3Cl)c(Cl)c2)ccc1O) `ZINC001184251740.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184251740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184251740/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001184251740 none COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2ccc(c3ccc(N)cc3Cl)c(Cl)c2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 16, 1, 16, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 5, 5, 3, 1, 1, 1, 1, 2, 2, 2, 12, 12, 10, 12, 22, 22, 22, 22, 22, 22, 22, 12, 12, 12, 5, 5, 5, 5, 10, 10, 10, 5, 3, 3, 2, 12, 12, 22, 22, 22, 22, 22, 12, 5, 5, 10] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184251740 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184251740/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184251740 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 139) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/139 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/139' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2ccc(c3ccc(N)cc3Cl)c(Cl)c2)ccc1O) `ZINC001184251740.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184251740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184251740/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001184251740 none COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2ccc(c3ccc(N)cc3Cl)c(Cl)c2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 16, 1, 16, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 5, 5, 3, 1, 1, 1, 1, 2, 2, 2, 12, 12, 12, 12, 22, 22, 22, 18, 22, 22, 22, 12, 12, 12, 5, 5, 5, 5, 10, 10, 10, 5, 3, 3, 2, 12, 12, 22, 22, 22, 22, 22, 12, 5, 5, 10] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184251740 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184251740 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184251740/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184251740/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184251740 Building ZINC001184251740 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184251740' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184251740 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184251740 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184251740/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184251740 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 138) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/138: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2ccc(c3ccc(N)cc3Cl)c(Cl)c2)ccc1O) `ZINC001184251740.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184251740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184251740/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001184251740 none COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2ccc(c3ccc(N)cc3Cl)c(Cl)c2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 16, 1, 16, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 5, 5, 3, 1, 1, 1, 1, 2, 2, 2, 12, 12, 10, 12, 22, 22, 22, 22, 22, 22, 22, 12, 12, 12, 5, 5, 5, 5, 10, 10, 10, 5, 3, 3, 2, 12, 12, 22, 22, 22, 22, 22, 12, 5, 5, 10] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184251740 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184251740/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184251740 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 139) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/139: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2ccc(c3ccc(N)cc3Cl)c(Cl)c2)ccc1O) `ZINC001184251740.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184251740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184251740/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001184251740 none COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2ccc(c3ccc(N)cc3Cl)c(Cl)c2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 16, 1, 16, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 5, 5, 3, 1, 1, 1, 1, 2, 2, 2, 12, 12, 12, 12, 22, 22, 22, 18, 22, 22, 22, 12, 12, 12, 5, 5, 5, 5, 10, 10, 10, 5, 3, 3, 2, 12, 12, 22, 22, 22, 22, 22, 12, 5, 5, 10] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184251740 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184251740 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184251740/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184251740/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184251740 Building ZINC001184252221 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184252221' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184252221 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184252221 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184252221/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184252221 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 140) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/140 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/140' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2ccc(Oc3ccc(C(F)(F)F)cc3)cc2)ccc1O) `ZINC001184252221.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184252221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184252221/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184252221 none COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2ccc(Oc3ccc(C(F)(F)F)cc3)cc2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 14, 26, 26, 26, 26, 26, 26, 26, 26, 26, 3, 3, 4, 4, 4, 4, 7, 7, 7, 4, 2, 2, 1, 3, 3, 26, 26, 26, 26, 3, 3, 4, 4, 8] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 38] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184252221 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184252221/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184252221 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 141) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/141 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/141' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2ccc(Oc3ccc(C(F)(F)F)cc3)cc2)ccc1O) `ZINC001184252221.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184252221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184252221/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184252221 none COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2ccc(Oc3ccc(C(F)(F)F)cc3)cc2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 2, 3, 18, 25, 25, 18, 18, 25, 25, 25, 25, 25, 3, 3, 4, 4, 4, 4, 7, 7, 7, 4, 2, 2, 1, 3, 3, 25, 25, 25, 25, 3, 3, 4, 4, 8] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 38] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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/129831/xbf-8058088.32/working/building/ZINC001184252221 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184252221 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184252221/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184252221/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184252221 Building ZINC001184252221 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184252221' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184252221 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184252221 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184252221/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184252221 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 140) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/140: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2ccc(Oc3ccc(C(F)(F)F)cc3)cc2)ccc1O) `ZINC001184252221.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184252221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184252221/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184252221 none COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2ccc(Oc3ccc(C(F)(F)F)cc3)cc2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 14, 26, 26, 26, 26, 26, 26, 26, 26, 26, 3, 3, 4, 4, 4, 4, 7, 7, 7, 4, 2, 2, 1, 3, 3, 26, 26, 26, 26, 3, 3, 4, 4, 8] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 38] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184252221 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184252221/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184252221 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 141) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/141: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2ccc(Oc3ccc(C(F)(F)F)cc3)cc2)ccc1O) `ZINC001184252221.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184252221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184252221/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184252221 none COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2ccc(Oc3ccc(C(F)(F)F)cc3)cc2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 2, 3, 18, 25, 25, 18, 18, 25, 25, 25, 25, 25, 3, 3, 4, 4, 4, 4, 7, 7, 7, 4, 2, 2, 1, 3, 3, 25, 25, 25, 25, 3, 3, 4, 4, 8] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 38] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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/129831/xbf-8058088.32/working/building/ZINC001184252221 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184252221 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184252221/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184252221/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184252221 Building ZINC001184253371 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184253371' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184253371 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184253371 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184253371/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184253371 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 142) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/142 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/142' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2cc(C)ccc2NCCCc2ccccc2)ccc1O) `ZINC001184253371.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184253371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184253371/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184253371 none COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2cc(C)ccc2NCCCc2ccccc2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 1, 1, 5, 1, 1, 1, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 5, 5, 5, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 3, 4, 4, 4, 8, 11, 24, 28, 28, 28, 28, 28, 28, 5, 5, 5, 5, 8, 8, 8, 5, 3, 3, 2, 4, 4, 4, 4, 4, 4, 8, 11, 11, 24, 24, 28, 28, 28, 28, 28, 28, 28, 5, 5, 10] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184253371 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184253371/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184253371 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 143) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/143 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/143' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2cc(C)ccc2NCCCc2ccccc2)ccc1O) `ZINC001184253371.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184253371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184253371/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184253371 none COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2cc(C)ccc2NCCCc2ccccc2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 1, 1, 5, 1, 1, 1, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 7, 10, 22, 26, 26, 26, 26, 26, 26, 5, 5, 5, 5, 10, 10, 10, 5, 3, 3, 1, 3, 3, 3, 3, 3, 3, 7, 10, 10, 22, 22, 26, 26, 26, 26, 26, 26, 26, 5, 5, 10] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 38] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184253371 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184253371 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184253371/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184253371/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184253371 Building ZINC001184253371 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184253371' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184253371 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184253371 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184253371/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184253371 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 142) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/142: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2cc(C)ccc2NCCCc2ccccc2)ccc1O) `ZINC001184253371.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184253371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184253371/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184253371 none COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2cc(C)ccc2NCCCc2ccccc2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 1, 1, 5, 1, 1, 1, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 5, 5, 5, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 3, 4, 4, 4, 8, 11, 24, 28, 28, 28, 28, 28, 28, 5, 5, 5, 5, 8, 8, 8, 5, 3, 3, 2, 4, 4, 4, 4, 4, 4, 8, 11, 11, 24, 24, 28, 28, 28, 28, 28, 28, 28, 5, 5, 10] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184253371 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184253371/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184253371 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 143) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/143: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2cc(C)ccc2NCCCc2ccccc2)ccc1O) `ZINC001184253371.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184253371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184253371/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184253371 none COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2cc(C)ccc2NCCCc2ccccc2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 1, 1, 5, 1, 1, 1, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 7, 10, 22, 26, 26, 26, 26, 26, 26, 5, 5, 5, 5, 10, 10, 10, 5, 3, 3, 1, 3, 3, 3, 3, 3, 3, 7, 10, 10, 22, 22, 26, 26, 26, 26, 26, 26, 26, 5, 5, 10] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 38] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184253371 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184253371 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184253371/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184253371/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184253371 Building ZINC001184253910 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184253910' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184253910 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184253910 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184253910/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184253910 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 144) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/144 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/144' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2c(C)c(C(F)(F)F)cc(Cl)c2Cl)ccc1O) `ZINC001184253910.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184253910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184253910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001184253910 none COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2c(C)c(C(F)(F)F)cc(Cl)c2Cl)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 1, 5, 1, 5, 15, 15, 15, 1, 1, 16, 1, 16, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [26, 14, 14, 14, 7, 1, 1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 7, 13, 13, 13, 13, 14, 14, 14, 14, 26, 26, 26, 14, 7, 7, 3, 13, 13, 13, 13, 14, 14, 28] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184253910 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184253910/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184253910 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 145) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/145 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/145' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2c(C)c(C(F)(F)F)cc(Cl)c2Cl)ccc1O) `ZINC001184253910.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184253910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184253910/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001184253910 none COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2c(C)c(C(F)(F)F)cc(Cl)c2Cl)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 1, 5, 1, 5, 15, 15, 15, 1, 1, 16, 1, 16, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [26, 14, 14, 14, 7, 1, 1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 11, 13, 13, 13, 13, 14, 14, 14, 14, 26, 26, 26, 14, 7, 7, 3, 13, 13, 13, 13, 14, 14, 28] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184253910 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184253910 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184253910/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184253910/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184253910 Building ZINC001184253910 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184253910' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184253910 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184253910 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184253910/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184253910 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 144) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/144: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2c(C)c(C(F)(F)F)cc(Cl)c2Cl)ccc1O) `ZINC001184253910.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184253910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184253910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001184253910 none COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2c(C)c(C(F)(F)F)cc(Cl)c2Cl)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 1, 5, 1, 5, 15, 15, 15, 1, 1, 16, 1, 16, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [26, 14, 14, 14, 7, 1, 1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 7, 13, 13, 13, 13, 14, 14, 14, 14, 26, 26, 26, 14, 7, 7, 3, 13, 13, 13, 13, 14, 14, 28] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184253910 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184253910/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184253910 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 145) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/145: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2c(C)c(C(F)(F)F)cc(Cl)c2Cl)ccc1O) `ZINC001184253910.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184253910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184253910/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001184253910 none COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2c(C)c(C(F)(F)F)cc(Cl)c2Cl)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 1, 5, 1, 5, 15, 15, 15, 1, 1, 16, 1, 16, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [26, 14, 14, 14, 7, 1, 1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 11, 13, 13, 13, 13, 14, 14, 14, 14, 26, 26, 26, 14, 7, 7, 3, 13, 13, 13, 13, 14, 14, 28] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184253910 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184253910 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184253910/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184253910/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184253910 Building ZINC001184254500 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254500' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254500 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184254500 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254500/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254500 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 146) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/146 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/146' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N[C@H](c2ccccc2)c2cccc3ccccc32)ccc1O) `ZINC001184254500.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184254500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254500/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184254500 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N[C@H](c2ccccc2)c2cccc3ccccc32)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [15, 7, 7, 7, 4, 1, 1, 1, 1, 3, 3, 3, 5, 5, 11, 11, 5, 11, 11, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 7, 7, 7, 15, 15, 15, 7, 4, 4, 3, 11, 11, 5, 11, 11, 13, 13, 13, 13, 13, 13, 13, 7, 7, 14] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 100 number of broken/clashed sets: 74 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254500 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254500/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254500 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 147) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/147 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/147' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)N[C@H](c2ccccc2)c2cccc3ccccc32)ccc1O) `ZINC001184254500.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184254500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254500/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184254500 none COc1cc(C[C@]([O-])([SiH3])C(=O)N[C@H](c2ccccc2)c2cccc3ccccc32)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [17, 6, 6, 6, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 9, 9, 5, 9, 9, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 6, 6, 17, 17, 17, 6, 3, 3, 3, 9, 9, 5, 9, 9, 12, 12, 12, 12, 12, 12, 12, 6, 6, 12] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 91 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254500 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184254500 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254500/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254500/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254500 Building ZINC001184254500 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254500' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254500 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184254500 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254500/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254500 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 146) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/146: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N[C@H](c2ccccc2)c2cccc3ccccc32)ccc1O) `ZINC001184254500.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184254500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254500/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184254500 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N[C@H](c2ccccc2)c2cccc3ccccc32)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [15, 7, 7, 7, 4, 1, 1, 1, 1, 3, 3, 3, 5, 5, 11, 11, 5, 11, 11, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 7, 7, 7, 15, 15, 15, 7, 4, 4, 3, 11, 11, 5, 11, 11, 13, 13, 13, 13, 13, 13, 13, 7, 7, 14] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 100 number of broken/clashed sets: 74 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254500 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254500/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254500 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 147) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/147: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)N[C@H](c2ccccc2)c2cccc3ccccc32)ccc1O) `ZINC001184254500.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184254500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254500/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184254500 none COc1cc(C[C@]([O-])([SiH3])C(=O)N[C@H](c2ccccc2)c2cccc3ccccc32)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [17, 6, 6, 6, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 9, 9, 5, 9, 9, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 6, 6, 17, 17, 17, 6, 3, 3, 3, 9, 9, 5, 9, 9, 12, 12, 12, 12, 12, 12, 12, 6, 6, 12] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 91 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254500 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184254500 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254500/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254500/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254500 Building ZINC001184254501 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254501' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254501 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184254501 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254501/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254501 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 148) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/148 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/148' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N[C@@H](c2ccccc2)c2cccc3ccccc32)ccc1O) `ZINC001184254501.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184254501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184254501 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N[C@@H](c2ccccc2)c2cccc3ccccc32)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [17, 6, 6, 6, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 9, 9, 6, 9, 9, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 6, 6, 17, 17, 17, 6, 3, 3, 3, 9, 9, 9, 9, 9, 12, 12, 12, 12, 12, 12, 12, 6, 6, 12] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 93 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254501 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254501/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254501 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 149) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/149 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/149' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)N[C@@H](c2ccccc2)c2cccc3ccccc32)ccc1O) `ZINC001184254501.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184254501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254501/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184254501 none COc1cc(C[C@]([O-])([SiH3])C(=O)N[C@@H](c2ccccc2)c2cccc3ccccc32)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [15, 7, 7, 7, 4, 1, 1, 1, 1, 3, 3, 3, 5, 5, 11, 11, 6, 11, 11, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 7, 7, 7, 15, 15, 15, 7, 4, 4, 3, 11, 11, 6, 11, 11, 13, 13, 13, 13, 13, 13, 13, 7, 7, 14] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 97 number of broken/clashed sets: 74 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254501 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184254501 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254501/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254501/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254501 Building ZINC001184254501 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254501' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254501 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184254501 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254501/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254501 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 148) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/148: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N[C@@H](c2ccccc2)c2cccc3ccccc32)ccc1O) `ZINC001184254501.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184254501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184254501 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N[C@@H](c2ccccc2)c2cccc3ccccc32)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [17, 6, 6, 6, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 9, 9, 6, 9, 9, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 6, 6, 17, 17, 17, 6, 3, 3, 3, 9, 9, 9, 9, 9, 12, 12, 12, 12, 12, 12, 12, 6, 6, 12] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 93 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254501 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254501/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254501 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 149) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/149: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)N[C@@H](c2ccccc2)c2cccc3ccccc32)ccc1O) `ZINC001184254501.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184254501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254501/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184254501 none COc1cc(C[C@]([O-])([SiH3])C(=O)N[C@@H](c2ccccc2)c2cccc3ccccc32)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [15, 7, 7, 7, 4, 1, 1, 1, 1, 3, 3, 3, 5, 5, 11, 11, 6, 11, 11, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 7, 7, 7, 15, 15, 15, 7, 4, 4, 3, 11, 11, 6, 11, 11, 13, 13, 13, 13, 13, 13, 13, 7, 7, 14] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 97 number of broken/clashed sets: 74 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254501 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184254501 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254501/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254501/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254501 Building ZINC001184254779 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254779' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254779 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184254779 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254779/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254779 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 150) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/150 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/150' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2ccc(Oc3c(Cl)cncc3Cl)cc2)ccc1O) `ZINC001184254779.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184254779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254779/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001184254779 none COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2ccc(Oc3c(Cl)cncc3Cl)cc2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 16, 1, 8, 1, 1, 16, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [8, 4, 4, 4, 2, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 2, 17, 23, 23, 23, 23, 23, 23, 23, 4, 4, 4, 4, 4, 4, 8, 8, 8, 4, 2, 2, 2, 4, 4, 23, 23, 4, 4, 4, 4, 8] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254779 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254779/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254779 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 151) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/151 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/151' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2ccc(Oc3c(Cl)cncc3Cl)cc2)ccc1O) `ZINC001184254779.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184254779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254779/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001184254779 none COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2ccc(Oc3c(Cl)cncc3Cl)cc2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 16, 1, 8, 1, 1, 16, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [8, 4, 4, 4, 2, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 3, 21, 22, 22, 22, 21, 22, 22, 22, 4, 4, 4, 4, 4, 4, 8, 8, 8, 4, 2, 2, 2, 4, 4, 22, 22, 4, 4, 4, 4, 8] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254779 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184254779 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254779/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254779/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254779 Building ZINC001184254779 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254779' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254779 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184254779 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254779/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254779 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 150) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/150: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2ccc(Oc3c(Cl)cncc3Cl)cc2)ccc1O) `ZINC001184254779.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184254779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254779/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001184254779 none COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2ccc(Oc3c(Cl)cncc3Cl)cc2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 16, 1, 8, 1, 1, 16, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [8, 4, 4, 4, 2, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 2, 17, 23, 23, 23, 23, 23, 23, 23, 4, 4, 4, 4, 4, 4, 8, 8, 8, 4, 2, 2, 2, 4, 4, 23, 23, 4, 4, 4, 4, 8] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254779 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254779/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254779 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 151) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/151: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2ccc(Oc3c(Cl)cncc3Cl)cc2)ccc1O) `ZINC001184254779.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184254779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254779/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001184254779 none COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2ccc(Oc3c(Cl)cncc3Cl)cc2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 16, 1, 8, 1, 1, 16, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [8, 4, 4, 4, 2, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 3, 21, 22, 22, 22, 21, 22, 22, 22, 4, 4, 4, 4, 4, 4, 8, 8, 8, 4, 2, 2, 2, 4, 4, 22, 22, 4, 4, 4, 4, 8] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254779 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184254779 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254779/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254779/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184254779 Building ZINC001184256502 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184256502' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184256502 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184256502 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184256502/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184256502 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 152) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/152 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/152' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cc(c2ccc(NC(=O)[C@@]([O-])([SiH3])Cc3ccc(O)c(OC)c3)c(CC)c2)ccc1N) `ZINC001184256502.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184256502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184256502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184256502 none CCc1cc(c2ccc(NC(=O)[C@@]([O-])([SiH3])Cc3ccc(O)c(OC)c3)c(CC)c2)ccc1N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 1, 5, 5, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [20, 12, 12, 12, 3, 2, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 5, 2, 3, 3, 5, 3, 12, 12, 12, 12, 20, 20, 20, 20, 20, 12, 3, 3, 1, 1, 1, 2, 2, 4, 5, 5, 5, 2, 5, 5, 5, 5, 5, 3, 12, 12, 12, 12] 100 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184256502 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184256502/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184256502 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 153) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/153 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/153' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cc(c2ccc(NC(=O)[C@]([O-])([SiH3])Cc3ccc(O)c(OC)c3)c(CC)c2)ccc1N) `ZINC001184256502.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184256502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184256502/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184256502 none CCc1cc(c2ccc(NC(=O)[C@]([O-])([SiH3])Cc3ccc(O)c(OC)c3)c(CC)c2)ccc1N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 1, 5, 5, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [20, 12, 12, 12, 3, 2, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 5, 3, 3, 3, 5, 3, 12, 12, 3, 3, 20, 20, 20, 20, 20, 12, 3, 3, 1, 2, 2, 3, 3, 6, 5, 5, 5, 3, 5, 5, 5, 5, 5, 3, 12, 12, 12, 12] 100 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184256502 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184256502 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184256502/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184256502/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184256502 Building ZINC001184256502 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184256502' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184256502 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184256502 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184256502/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184256502 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 152) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/152: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cc(c2ccc(NC(=O)[C@@]([O-])([SiH3])Cc3ccc(O)c(OC)c3)c(CC)c2)ccc1N) `ZINC001184256502.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184256502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184256502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184256502 none CCc1cc(c2ccc(NC(=O)[C@@]([O-])([SiH3])Cc3ccc(O)c(OC)c3)c(CC)c2)ccc1N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 1, 5, 5, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [20, 12, 12, 12, 3, 2, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 5, 2, 3, 3, 5, 3, 12, 12, 12, 12, 20, 20, 20, 20, 20, 12, 3, 3, 1, 1, 1, 2, 2, 4, 5, 5, 5, 2, 5, 5, 5, 5, 5, 3, 12, 12, 12, 12] 100 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184256502 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184256502/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184256502 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 153) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/153: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cc(c2ccc(NC(=O)[C@]([O-])([SiH3])Cc3ccc(O)c(OC)c3)c(CC)c2)ccc1N) `ZINC001184256502.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184256502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184256502/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184256502 none CCc1cc(c2ccc(NC(=O)[C@]([O-])([SiH3])Cc3ccc(O)c(OC)c3)c(CC)c2)ccc1N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 1, 5, 5, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [20, 12, 12, 12, 3, 2, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 5, 3, 3, 3, 5, 3, 12, 12, 3, 3, 20, 20, 20, 20, 20, 12, 3, 3, 1, 2, 2, 3, 3, 6, 5, 5, 5, 3, 5, 5, 5, 5, 5, 3, 12, 12, 12, 12] 100 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184256502 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184256502 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184256502/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184256502/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184256502 Building ZINC001184315697 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184315697' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184315697 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184315697 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184315697/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184315697 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 154) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/154 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/154' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@]([O-])([SiH3])C(=O)Nc1ncnc2c1c(c1cccc3ccccc31)nn2C(C)(C)C) `ZINC001184315697.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184315697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184315697/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184315697 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)Nc1ncnc2c1c(c1cccc3ccccc31)nn2C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 4, 4, 4, 11, 11, 11, 11, 11, 11, 11, 38, 38, 38, 38, 38, 38, 38, 38, 38, 11, 11, 11, 20, 20, 20, 5, 5, 5, 5, 5, 5, 5, 5, 4, 11, 38, 38, 38, 38, 38, 38, 38, 20, 20, 20, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184315697 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184315697/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184315697 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 155) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/155 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/155' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@]([O-])([SiH3])C(=O)Nc1ncnc2c1c(c1cccc3ccccc31)nn2C(C)(C)C) `ZINC001184315697.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184315697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184315697/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184315697 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)Nc1ncnc2c1c(c1cccc3ccccc31)nn2C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 6, 6, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 34, 34, 34, 34, 34, 34, 34, 34, 34, 10, 10, 10, 21, 21, 21, 6, 6, 6, 6, 6, 6, 6, 6, 3, 10, 34, 34, 34, 34, 34, 34, 34, 21, 21, 21, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184315697 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184315697 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184315697/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184315697/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184315697 Building ZINC001184315697 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184315697' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184315697 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184315697 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184315697/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184315697 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 154) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/154: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@]([O-])([SiH3])C(=O)Nc1ncnc2c1c(c1cccc3ccccc31)nn2C(C)(C)C) `ZINC001184315697.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184315697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184315697/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184315697 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)Nc1ncnc2c1c(c1cccc3ccccc31)nn2C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 4, 4, 4, 11, 11, 11, 11, 11, 11, 11, 38, 38, 38, 38, 38, 38, 38, 38, 38, 11, 11, 11, 20, 20, 20, 5, 5, 5, 5, 5, 5, 5, 5, 4, 11, 38, 38, 38, 38, 38, 38, 38, 20, 20, 20, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184315697 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184315697/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184315697 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 155) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/155: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@]([O-])([SiH3])C(=O)Nc1ncnc2c1c(c1cccc3ccccc31)nn2C(C)(C)C) `ZINC001184315697.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184315697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184315697/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184315697 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)Nc1ncnc2c1c(c1cccc3ccccc31)nn2C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 6, 6, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 34, 34, 34, 34, 34, 34, 34, 34, 34, 10, 10, 10, 21, 21, 21, 6, 6, 6, 6, 6, 6, 6, 6, 3, 10, 34, 34, 34, 34, 34, 34, 34, 21, 21, 21, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184315697 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184315697 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184315697/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184315697/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184315697 Building ZINC001184315699 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184315699' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184315699 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184315699 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184315699/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184315699 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 156) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/156 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/156' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)Nc1ncnc2c1c(c1cccc3ccccc31)nn2C(C)(C)C) `ZINC001184315699.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184315699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184315699/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184315699 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)Nc1ncnc2c1c(c1cccc3ccccc31)nn2C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 6, 6, 1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 36, 36, 36, 36, 36, 36, 36, 36, 36, 11, 11, 11, 23, 23, 23, 6, 6, 6, 6, 6, 6, 6, 6, 3, 11, 36, 36, 36, 36, 36, 36, 36, 23, 23, 23, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184315699 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184315699/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184315699 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 157) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/157 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/157' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@]([O-])([SiH3])C(=O)Nc1ncnc2c1c(c1cccc3ccccc31)nn2C(C)(C)C) `ZINC001184315699.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184315699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184315699/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184315699 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)Nc1ncnc2c1c(c1cccc3ccccc31)nn2C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 4, 4, 4, 11, 11, 11, 11, 11, 11, 11, 35, 35, 35, 35, 35, 35, 35, 35, 35, 11, 11, 11, 19, 19, 19, 5, 5, 5, 5, 5, 5, 5, 5, 4, 11, 35, 35, 35, 35, 35, 35, 35, 19, 19, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184315699 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184315699 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184315699/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184315699/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184315699 Building ZINC001184315699 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184315699' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184315699 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184315699 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184315699/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184315699 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 156) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/156: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)Nc1ncnc2c1c(c1cccc3ccccc31)nn2C(C)(C)C) `ZINC001184315699.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184315699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184315699/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184315699 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)Nc1ncnc2c1c(c1cccc3ccccc31)nn2C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 6, 6, 1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 36, 36, 36, 36, 36, 36, 36, 36, 36, 11, 11, 11, 23, 23, 23, 6, 6, 6, 6, 6, 6, 6, 6, 3, 11, 36, 36, 36, 36, 36, 36, 36, 23, 23, 23, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184315699 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184315699/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184315699 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 157) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/157: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@]([O-])([SiH3])C(=O)Nc1ncnc2c1c(c1cccc3ccccc31)nn2C(C)(C)C) `ZINC001184315699.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184315699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184315699/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184315699 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)Nc1ncnc2c1c(c1cccc3ccccc31)nn2C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 4, 4, 4, 11, 11, 11, 11, 11, 11, 11, 35, 35, 35, 35, 35, 35, 35, 35, 35, 11, 11, 11, 19, 19, 19, 5, 5, 5, 5, 5, 5, 5, 5, 4, 11, 35, 35, 35, 35, 35, 35, 35, 19, 19, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184315699 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184315699 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184315699/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184315699/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184315699 Building ZINC001184317316 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184317316' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184317316 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184317316 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184317316/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184317316 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 158) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/158 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/158' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@]([O-])([SiH3])C(=O)N(CCc1cc(OC)c(Cl)cc1OC)Cc1ccccc1OC) `ZINC001184317316.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184317316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184317316/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184317316 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)N(CCc1cc(OC)c(Cl)cc1OC)Cc1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 12, 5, 1, 16, 1, 1, 12, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 2, 2, 4, 9, 9, 28, 28, 28, 47, 28, 28, 28, 28, 28, 40, 4, 5, 5, 5, 5, 5, 5, 5, 9, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9, 28, 47, 47, 47, 28, 40, 40, 40, 5, 5, 5, 5, 5, 5, 9, 9, 9] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 139 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184317316 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184317316/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184317316 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 159) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/159 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/159' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@]([O-])([SiH3])C(=O)N(CCc1cc(OC)c(Cl)cc1OC)Cc1ccccc1OC) `ZINC001184317316.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184317316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184317316/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184317316 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)N(CCc1cc(OC)c(Cl)cc1OC)Cc1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 12, 5, 1, 16, 1, 1, 12, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 2, 2, 3, 6, 6, 21, 21, 21, 39, 21, 21, 21, 21, 21, 37, 3, 6, 6, 6, 6, 6, 6, 6, 10, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 21, 39, 39, 39, 21, 37, 37, 37, 6, 6, 6, 6, 6, 6, 10, 10, 10] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 135 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184317316 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184317316 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184317316/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184317316/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184317316 Building ZINC001184317316 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184317316' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184317316 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184317316 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184317316/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184317316 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 158) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/158: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@]([O-])([SiH3])C(=O)N(CCc1cc(OC)c(Cl)cc1OC)Cc1ccccc1OC) `ZINC001184317316.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184317316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184317316/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184317316 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)N(CCc1cc(OC)c(Cl)cc1OC)Cc1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 12, 5, 1, 16, 1, 1, 12, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 2, 2, 4, 9, 9, 28, 28, 28, 47, 28, 28, 28, 28, 28, 40, 4, 5, 5, 5, 5, 5, 5, 5, 9, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9, 28, 47, 47, 47, 28, 40, 40, 40, 5, 5, 5, 5, 5, 5, 9, 9, 9] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 139 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184317316 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184317316/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184317316 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 159) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/159: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@]([O-])([SiH3])C(=O)N(CCc1cc(OC)c(Cl)cc1OC)Cc1ccccc1OC) `ZINC001184317316.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184317316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184317316/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184317316 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)N(CCc1cc(OC)c(Cl)cc1OC)Cc1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 12, 5, 1, 16, 1, 1, 12, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 2, 2, 3, 6, 6, 21, 21, 21, 39, 21, 21, 21, 21, 21, 37, 3, 6, 6, 6, 6, 6, 6, 6, 10, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 21, 39, 39, 39, 21, 37, 37, 37, 6, 6, 6, 6, 6, 6, 10, 10, 10] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 135 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184317316 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184317316 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184317316/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184317316/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184317316 Building ZINC001184317317 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184317317' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184317317 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184317317 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184317317/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184317317 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 160) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/160 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/160' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)N(CCc1cc(OC)c(Cl)cc1OC)Cc1ccccc1OC) `ZINC001184317317.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184317317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184317317/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184317317 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)N(CCc1cc(OC)c(Cl)cc1OC)Cc1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 12, 5, 1, 16, 1, 1, 12, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 2, 2, 4, 9, 9, 28, 28, 28, 48, 28, 28, 28, 28, 28, 41, 4, 5, 5, 5, 5, 5, 5, 5, 10, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9, 28, 48, 48, 48, 28, 41, 41, 41, 5, 5, 5, 5, 5, 5, 10, 10, 10] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 144 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184317317 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184317317/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184317317 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 161) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/161 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/161' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@]([O-])([SiH3])C(=O)N(CCc1cc(OC)c(Cl)cc1OC)Cc1ccccc1OC) `ZINC001184317317.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184317317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184317317/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184317317 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)N(CCc1cc(OC)c(Cl)cc1OC)Cc1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 12, 5, 1, 16, 1, 1, 12, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 2, 5, 5, 20, 20, 20, 39, 20, 20, 20, 20, 20, 36, 2, 5, 5, 5, 5, 5, 5, 5, 9, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 20, 39, 39, 39, 20, 36, 36, 36, 5, 5, 5, 5, 5, 5, 9, 9, 9] 50 rigid atoms, others: [0, 1, 34, 35, 32, 5, 38, 33, 8, 9, 39, 2, 3, 7, 36, 6, 4, 37] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184317317 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184317317 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184317317/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184317317/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184317317 Building ZINC001184317317 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184317317' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184317317 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184317317 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184317317/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184317317 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 160) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/160: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)N(CCc1cc(OC)c(Cl)cc1OC)Cc1ccccc1OC) `ZINC001184317317.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184317317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184317317/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184317317 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)N(CCc1cc(OC)c(Cl)cc1OC)Cc1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 12, 5, 1, 16, 1, 1, 12, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 2, 2, 4, 9, 9, 28, 28, 28, 48, 28, 28, 28, 28, 28, 41, 4, 5, 5, 5, 5, 5, 5, 5, 10, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9, 28, 48, 48, 48, 28, 41, 41, 41, 5, 5, 5, 5, 5, 5, 10, 10, 10] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 144 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184317317 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184317317/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184317317 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 161) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/161: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@]([O-])([SiH3])C(=O)N(CCc1cc(OC)c(Cl)cc1OC)Cc1ccccc1OC) `ZINC001184317317.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184317317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184317317/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184317317 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)N(CCc1cc(OC)c(Cl)cc1OC)Cc1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 12, 5, 1, 16, 1, 1, 12, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 2, 5, 5, 20, 20, 20, 39, 20, 20, 20, 20, 20, 36, 2, 5, 5, 5, 5, 5, 5, 5, 9, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 20, 39, 39, 39, 20, 36, 36, 36, 5, 5, 5, 5, 5, 5, 9, 9, 9] 50 rigid atoms, others: [0, 1, 34, 35, 32, 5, 38, 33, 8, 9, 39, 2, 3, 7, 36, 6, 4, 37] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184317317 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184317317 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184317317/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184317317/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184317317 Building ZINC001184358268 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184358268' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184358268 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184358268 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184358268/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184358268 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 162) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/162 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/162' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(Sc2ccc(N3CCN(C(=O)[C@@]([O-])([SiH3])c4ccccc4)CC3)cc2)c(C)c1) `ZINC001184358268.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184358268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184358268/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184358268 none Cc1ccc(Sc2ccc(N3CCN(C(=O)[C@@]([O-])([SiH3])c4ccccc4)CC3)cc2)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 48, 50, 32, 5, 5, 17, 17, 5, 5, 5, 5, 4, 2, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 5, 5, 5, 5, 1, 1, 1, 1, 1, 5, 5, 5, 5, 17, 17, 50, 50, 50, 50] 50 rigid atoms, others: [42, 43, 44, 45, 46, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184358268 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184358268/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184358268 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 163) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/163 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/163' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(Sc2ccc(N3CCN(C(=O)[C@]([O-])([SiH3])c4ccccc4)CC3)cc2)c(C)c1) `ZINC001184358268.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184358268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184358268/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184358268 none Cc1ccc(Sc2ccc(N3CCN(C(=O)[C@]([O-])([SiH3])c4ccccc4)CC3)cc2)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 50, 50, 34, 4, 4, 16, 16, 4, 4, 4, 4, 3, 2, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 4, 4, 4, 4, 1, 1, 1, 1, 1, 4, 4, 4, 4, 16, 16, 50, 50, 50, 50] 50 rigid atoms, others: [42, 43, 44, 45, 46, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184358268 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184358268 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184358268/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184358268/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184358268 Building ZINC001184358268 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184358268' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184358268 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184358268 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184358268/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184358268 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 162) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/162: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(Sc2ccc(N3CCN(C(=O)[C@@]([O-])([SiH3])c4ccccc4)CC3)cc2)c(C)c1) `ZINC001184358268.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184358268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184358268/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184358268 none Cc1ccc(Sc2ccc(N3CCN(C(=O)[C@@]([O-])([SiH3])c4ccccc4)CC3)cc2)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 48, 50, 32, 5, 5, 17, 17, 5, 5, 5, 5, 4, 2, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 5, 5, 5, 5, 1, 1, 1, 1, 1, 5, 5, 5, 5, 17, 17, 50, 50, 50, 50] 50 rigid atoms, others: [42, 43, 44, 45, 46, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184358268 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184358268/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184358268 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 163) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/163: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(Sc2ccc(N3CCN(C(=O)[C@]([O-])([SiH3])c4ccccc4)CC3)cc2)c(C)c1) `ZINC001184358268.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184358268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184358268/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184358268 none Cc1ccc(Sc2ccc(N3CCN(C(=O)[C@]([O-])([SiH3])c4ccccc4)CC3)cc2)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 50, 50, 34, 4, 4, 16, 16, 4, 4, 4, 4, 3, 2, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 4, 4, 4, 4, 1, 1, 1, 1, 1, 4, 4, 4, 4, 16, 16, 50, 50, 50, 50] 50 rigid atoms, others: [42, 43, 44, 45, 46, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184358268 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184358268 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184358268/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184358268/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184358268 Building ZINC001184320244 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184320244' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184320244 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184320244 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184320244/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184320244 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 164) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/164 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/164' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@]([O-])([SiH3])C(=O)N1CCC2(CN(C(=O)OC(C)(C)C)c3ccc(Cl)cc32)CC1) `ZINC001184320244.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184320244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184320244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184320244 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)N1CCC2(CN(C(=O)OC(C)(C)C)c3ccc(Cl)cc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 6, 15, 19, 19, 19, 19, 19, 19, 29, 29, 49, 49, 49, 49, 19, 19, 19, 19, 19, 19, 19, 19, 19, 3, 3, 3, 3, 3, 3, 3, 3, 19, 19, 19, 19, 19, 19, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 104 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184320244 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184320244/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184320244 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 165) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/165 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/165' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@]([O-])([SiH3])C(=O)N1CCC2(CN(C(=O)OC(C)(C)C)c3ccc(Cl)cc32)CC1) `ZINC001184320244.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184320244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184320244/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184320244 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)N1CCC2(CN(C(=O)OC(C)(C)C)c3ccc(Cl)cc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 6, 16, 19, 19, 19, 19, 19, 19, 30, 30, 50, 50, 50, 50, 19, 19, 19, 19, 19, 19, 19, 19, 19, 2, 2, 2, 2, 2, 2, 2, 2, 19, 19, 19, 19, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 104 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184320244 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184320244 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184320244/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184320244/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184320244 Building ZINC001184320244 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184320244' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184320244 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184320244 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184320244/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184320244 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 164) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/164: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@]([O-])([SiH3])C(=O)N1CCC2(CN(C(=O)OC(C)(C)C)c3ccc(Cl)cc32)CC1) `ZINC001184320244.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184320244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184320244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184320244 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)N1CCC2(CN(C(=O)OC(C)(C)C)c3ccc(Cl)cc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 6, 15, 19, 19, 19, 19, 19, 19, 29, 29, 49, 49, 49, 49, 19, 19, 19, 19, 19, 19, 19, 19, 19, 3, 3, 3, 3, 3, 3, 3, 3, 19, 19, 19, 19, 19, 19, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 104 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184320244 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184320244/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184320244 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 165) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/165: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@]([O-])([SiH3])C(=O)N1CCC2(CN(C(=O)OC(C)(C)C)c3ccc(Cl)cc32)CC1) `ZINC001184320244.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184320244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184320244/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184320244 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)N1CCC2(CN(C(=O)OC(C)(C)C)c3ccc(Cl)cc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 6, 16, 19, 19, 19, 19, 19, 19, 30, 30, 50, 50, 50, 50, 19, 19, 19, 19, 19, 19, 19, 19, 19, 2, 2, 2, 2, 2, 2, 2, 2, 19, 19, 19, 19, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 104 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184320244 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184320244 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184320244/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184320244/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184320244 Building ZINC001184320251 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184320251' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184320251 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184320251 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184320251/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184320251 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 166) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/166 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/166' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)N1CCC2(CN(C(=O)OC(C)(C)C)c3ccc(Cl)cc32)CC1) `ZINC001184320251.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184320251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184320251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184320251 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)N1CCC2(CN(C(=O)OC(C)(C)C)c3ccc(Cl)cc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 6, 15, 19, 19, 19, 19, 19, 19, 31, 31, 50, 50, 50, 50, 19, 19, 19, 19, 19, 19, 19, 19, 19, 2, 2, 2, 2, 2, 2, 2, 2, 19, 19, 19, 19, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 105 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184320251 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184320251/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184320251 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 167) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/167 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/167' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@]([O-])([SiH3])C(=O)N1CCC2(CN(C(=O)OC(C)(C)C)c3ccc(Cl)cc32)CC1) `ZINC001184320251.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184320251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184320251/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184320251 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)N1CCC2(CN(C(=O)OC(C)(C)C)c3ccc(Cl)cc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 6, 16, 19, 19, 19, 19, 19, 19, 30, 30, 50, 50, 50, 50, 19, 19, 19, 19, 19, 19, 19, 19, 19, 2, 2, 2, 2, 2, 2, 2, 2, 19, 19, 19, 19, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 104 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184320251 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184320251 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184320251/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184320251/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184320251 Building ZINC001184320251 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184320251' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184320251 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184320251 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184320251/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184320251 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 166) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/166: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)N1CCC2(CN(C(=O)OC(C)(C)C)c3ccc(Cl)cc32)CC1) `ZINC001184320251.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184320251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184320251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184320251 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)N1CCC2(CN(C(=O)OC(C)(C)C)c3ccc(Cl)cc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 6, 15, 19, 19, 19, 19, 19, 19, 31, 31, 50, 50, 50, 50, 19, 19, 19, 19, 19, 19, 19, 19, 19, 2, 2, 2, 2, 2, 2, 2, 2, 19, 19, 19, 19, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 105 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184320251 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184320251/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184320251 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 167) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/167: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@]([O-])([SiH3])C(=O)N1CCC2(CN(C(=O)OC(C)(C)C)c3ccc(Cl)cc32)CC1) `ZINC001184320251.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184320251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184320251/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184320251 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)N1CCC2(CN(C(=O)OC(C)(C)C)c3ccc(Cl)cc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 6, 16, 19, 19, 19, 19, 19, 19, 30, 30, 50, 50, 50, 50, 19, 19, 19, 19, 19, 19, 19, 19, 19, 2, 2, 2, 2, 2, 2, 2, 2, 19, 19, 19, 19, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 104 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184320251 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184320251 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184320251/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184320251/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184320251 Building ZINC001184323061 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323061' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323061 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184323061 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323061/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323061 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 168) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/168 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/168' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCC(=O)c3cc(Cl)ccc32)c(C)c1) `ZINC001184323061.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184323061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323061/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184323061 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCC(=O)c3cc(Cl)ccc32)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 1, 11, 1, 1, 1, 16, 1, 1, 1, 1, 5, 1, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 3, 3, 3, 10, 10, 3, 4, 22, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 3, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323061 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323061/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323061 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 169) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/169 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/169' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCC(=O)c3cc(Cl)ccc32)c(C)c1) `ZINC001184323061.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184323061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323061/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184323061 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCC(=O)c3cc(Cl)ccc32)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 1, 11, 1, 1, 1, 16, 1, 1, 1, 1, 5, 1, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 3, 3, 3, 10, 10, 4, 14, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 3, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323061 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184323061 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323061/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323061/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323061 Building ZINC001184323061 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323061' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323061 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184323061 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323061/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323061 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 168) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/168: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCC(=O)c3cc(Cl)ccc32)c(C)c1) `ZINC001184323061.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184323061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323061/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184323061 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCC(=O)c3cc(Cl)ccc32)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 1, 11, 1, 1, 1, 16, 1, 1, 1, 1, 5, 1, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 3, 3, 3, 10, 10, 3, 4, 22, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 3, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323061 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323061/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323061 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 169) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/169: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCC(=O)c3cc(Cl)ccc32)c(C)c1) `ZINC001184323061.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184323061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323061/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184323061 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCC(=O)c3cc(Cl)ccc32)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 1, 11, 1, 1, 1, 16, 1, 1, 1, 1, 5, 1, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 3, 3, 3, 10, 10, 4, 14, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 3, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323061 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184323061 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323061/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323061/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323061 Building ZINC001184323070 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323070' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323070 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184323070 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323070/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323070 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 170) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/170 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/170' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCC(=O)c3cc(Cl)ccc32)c(C)c1) `ZINC001184323070.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184323070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184323070 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCC(=O)c3cc(Cl)ccc32)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 1, 11, 1, 1, 1, 16, 1, 1, 1, 1, 5, 1, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 3, 3, 3, 10, 10, 3, 4, 22, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 3, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323070 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323070/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323070 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 171) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/171 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/171' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCC(=O)c3cc(Cl)ccc32)c(C)c1) `ZINC001184323070.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184323070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323070/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184323070 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCC(=O)c3cc(Cl)ccc32)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 1, 11, 1, 1, 1, 16, 1, 1, 1, 1, 5, 1, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 3, 3, 3, 10, 10, 10, 14, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 3, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323070 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184323070 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323070/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323070/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323070 Building ZINC001184323070 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323070' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323070 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184323070 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323070/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323070 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 170) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/170: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCC(=O)c3cc(Cl)ccc32)c(C)c1) `ZINC001184323070.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184323070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184323070 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCC(=O)c3cc(Cl)ccc32)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 1, 11, 1, 1, 1, 16, 1, 1, 1, 1, 5, 1, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 3, 3, 3, 10, 10, 3, 4, 22, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 3, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323070 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323070/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323070 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 171) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/171: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCC(=O)c3cc(Cl)ccc32)c(C)c1) `ZINC001184323070.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184323070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323070/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184323070 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCC(=O)c3cc(Cl)ccc32)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 1, 11, 1, 1, 1, 16, 1, 1, 1, 1, 5, 1, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 3, 3, 3, 10, 10, 10, 14, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 3, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323070 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184323070 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323070/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323070/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323070 Building ZINC001184323277 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323277' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323277 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184323277 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323277/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323277 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 172) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/172 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/172' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@]([O-])([SiH3])C(=O)N(Cc1ccc(C)cc1)[C@H]1CC[C@H](NC(=O)OC(C)(C)C)CC1) `ZINC001184323277.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184323277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323277/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC001184323277 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)N(Cc1ccc(C)cc1)[C@H]1CC[C@H](NC(=O)OC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 1, 1, 5, 7, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 4, 6, 6, 5, 6, 6, 6, 4, 4, 4, 4, 4, 4, 4, 17, 28, 28, 44, 44, 44, 44, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 6, 6, 6, 6, 6, 6, 6, 4, 4, 4, 4, 17, 44, 44, 44, 44, 44, 44, 44, 44, 44, 4, 4, 4, 4] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 134 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323277 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323277/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323277 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 173) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/173 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/173' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)N(Cc1ccc(C)cc1)[C@H]1CC[C@H](NC(=O)OC(C)(C)C)CC1) `ZINC001184323277.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184323277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323277/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC001184323277 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)N(Cc1ccc(C)cc1)[C@H]1CC[C@H](NC(=O)OC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 1, 1, 5, 7, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 2, 2, 4, 4, 7, 7, 4, 4, 7, 7, 4, 4, 4, 4, 4, 4, 4, 17, 27, 27, 49, 50, 50, 50, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 7, 7, 7, 7, 7, 7, 7, 4, 4, 4, 4, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 168 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323277 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184323277 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323277/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323277/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323277 Building ZINC001184323277 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323277' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323277 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184323277 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323277/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323277 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 172) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/172: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@]([O-])([SiH3])C(=O)N(Cc1ccc(C)cc1)[C@H]1CC[C@H](NC(=O)OC(C)(C)C)CC1) `ZINC001184323277.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184323277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323277/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC001184323277 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)N(Cc1ccc(C)cc1)[C@H]1CC[C@H](NC(=O)OC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 1, 1, 5, 7, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 4, 4, 6, 6, 5, 6, 6, 6, 4, 4, 4, 4, 4, 4, 4, 17, 28, 28, 44, 44, 44, 44, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 6, 6, 6, 6, 6, 6, 6, 4, 4, 4, 4, 17, 44, 44, 44, 44, 44, 44, 44, 44, 44, 4, 4, 4, 4] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 134 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323277 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323277/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323277 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 173) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/173: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)N(Cc1ccc(C)cc1)[C@H]1CC[C@H](NC(=O)OC(C)(C)C)CC1) `ZINC001184323277.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184323277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323277/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC001184323277 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)N(Cc1ccc(C)cc1)[C@H]1CC[C@H](NC(=O)OC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 1, 1, 5, 7, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 2, 2, 4, 4, 7, 7, 4, 4, 7, 7, 4, 4, 4, 4, 4, 4, 4, 17, 27, 27, 49, 50, 50, 50, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 7, 7, 7, 7, 7, 7, 7, 4, 4, 4, 4, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 168 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323277 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184323277 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323277/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323277/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323277 Building ZINC001184323278 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323278' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323278 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184323278 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323278/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323278 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 174) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/174 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/174' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@]([O-])([SiH3])C(=O)N(Cc1ccc(C)cc1)[C@H]1CC[C@H](NC(=O)OC(C)(C)C)CC1) `ZINC001184323278.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184323278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323278/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC001184323278 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)N(Cc1ccc(C)cc1)[C@H]1CC[C@H](NC(=O)OC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 1, 1, 5, 7, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 6, 6, 8, 8, 7, 7, 8, 8, 6, 6, 6, 6, 6, 6, 6, 20, 32, 32, 48, 48, 48, 48, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 8, 8, 8, 8, 8, 8, 8, 6, 6, 6, 6, 20, 48, 48, 48, 48, 48, 48, 48, 48, 48, 6, 6, 6, 6] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 152 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323278 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323278/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323278 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 175) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/175 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/175' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@]([O-])([SiH3])C(=O)N(Cc1ccc(C)cc1)[C@H]1CC[C@H](NC(=O)OC(C)(C)C)CC1) `ZINC001184323278.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184323278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323278/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC001184323278 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)N(Cc1ccc(C)cc1)[C@H]1CC[C@H](NC(=O)OC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 1, 1, 5, 7, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 2, 2, 4, 4, 7, 7, 4, 4, 7, 7, 4, 4, 4, 4, 4, 4, 4, 18, 27, 27, 49, 50, 50, 50, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 7, 7, 7, 7, 7, 7, 7, 4, 4, 4, 4, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 167 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323278 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184323278 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323278/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323278/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323278 Building ZINC001184323278 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323278' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323278 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184323278 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323278/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323278 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 174) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/174: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@]([O-])([SiH3])C(=O)N(Cc1ccc(C)cc1)[C@H]1CC[C@H](NC(=O)OC(C)(C)C)CC1) `ZINC001184323278.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184323278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323278/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC001184323278 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)N(Cc1ccc(C)cc1)[C@H]1CC[C@H](NC(=O)OC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 1, 1, 5, 7, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 6, 6, 8, 8, 7, 7, 8, 8, 6, 6, 6, 6, 6, 6, 6, 20, 32, 32, 48, 48, 48, 48, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 8, 8, 8, 8, 8, 8, 8, 6, 6, 6, 6, 20, 48, 48, 48, 48, 48, 48, 48, 48, 48, 6, 6, 6, 6] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 152 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323278 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323278/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323278 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 175) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/175: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@]([O-])([SiH3])C(=O)N(Cc1ccc(C)cc1)[C@H]1CC[C@H](NC(=O)OC(C)(C)C)CC1) `ZINC001184323278.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184323278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323278/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC001184323278 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)N(Cc1ccc(C)cc1)[C@H]1CC[C@H](NC(=O)OC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 1, 1, 5, 7, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 2, 2, 4, 4, 7, 7, 4, 4, 7, 7, 4, 4, 4, 4, 4, 4, 4, 18, 27, 27, 49, 50, 50, 50, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 7, 7, 7, 7, 7, 7, 7, 4, 4, 4, 4, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 167 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323278 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184323278 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323278/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323278/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184323278 Building ZINC001184324396 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184324396' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184324396 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184324396 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184324396/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184324396 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 176) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/176 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/176' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)Nc1ncnc2c1c(c1cccc3ccccc31)nn2C(C)(C)C) `ZINC001184324396.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184324396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184324396/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184324396 none CC(C)C[C@@]([O-])([SiH3])C(=O)Nc1ncnc2c1c(c1cccc3ccccc31)nn2C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 16, 16, 16, 16, 44, 44, 44, 44, 44, 44, 44, 44, 44, 16, 16, 16, 26, 26, 26, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 16, 44, 44, 44, 44, 44, 44, 44, 26, 26, 26, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 131 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184324396 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184324396/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184324396 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 177) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/177 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/177' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)Nc1ncnc2c1c(c1cccc3ccccc31)nn2C(C)(C)C) `ZINC001184324396.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184324396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184324396/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184324396 none CC(C)C[C@]([O-])([SiH3])C(=O)Nc1ncnc2c1c(c1cccc3ccccc31)nn2C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 10, 10, 10, 10, 27, 27, 27, 27, 27, 27, 27, 27, 27, 10, 10, 10, 15, 15, 15, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 10, 27, 27, 27, 27, 27, 27, 27, 15, 15, 15, 15, 15, 15, 15, 15, 15] 27 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184324396 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184324396 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184324396/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184324396/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184324396 Building ZINC001184324396 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184324396' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184324396 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184324396 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184324396/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184324396 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 176) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/176: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)Nc1ncnc2c1c(c1cccc3ccccc31)nn2C(C)(C)C) `ZINC001184324396.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184324396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184324396/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184324396 none CC(C)C[C@@]([O-])([SiH3])C(=O)Nc1ncnc2c1c(c1cccc3ccccc31)nn2C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 16, 16, 16, 16, 44, 44, 44, 44, 44, 44, 44, 44, 44, 16, 16, 16, 26, 26, 26, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 16, 44, 44, 44, 44, 44, 44, 44, 26, 26, 26, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 131 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184324396 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184324396/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184324396 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 177) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/177: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)Nc1ncnc2c1c(c1cccc3ccccc31)nn2C(C)(C)C) `ZINC001184324396.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184324396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184324396/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184324396 none CC(C)C[C@]([O-])([SiH3])C(=O)Nc1ncnc2c1c(c1cccc3ccccc31)nn2C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 10, 10, 10, 10, 27, 27, 27, 27, 27, 27, 27, 27, 27, 10, 10, 10, 15, 15, 15, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 10, 27, 27, 27, 27, 27, 27, 27, 15, 15, 15, 15, 15, 15, 15, 15, 15] 27 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184324396 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184324396 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184324396/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184324396/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184324396 Building ZINC001184328307 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184328307' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184328307 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184328307 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184328307/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184328307 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 178) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/178 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/178' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)N1CCC2(CN(C(=O)OC(C)(C)C)c3ccc(Cl)cc32)CC1) `ZINC001184328307.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184328307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184328307/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184328307 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CCC2(CN(C(=O)OC(C)(C)C)c3ccc(Cl)cc32)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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 3, 7, 13, 13, 13, 13, 13, 13, 28, 28, 49, 49, 49, 49, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13, 13, 13, 49, 49, 49, 49, 49, 49, 49, 49, 49, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184328307 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184328307/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184328307 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 179) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/179 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/179' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)N1CCC2(CN(C(=O)OC(C)(C)C)c3ccc(Cl)cc32)CC1) `ZINC001184328307.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184328307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184328307/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184328307 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CCC2(CN(C(=O)OC(C)(C)C)c3ccc(Cl)cc32)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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 5, 12, 15, 15, 15, 15, 15, 15, 26, 26, 50, 50, 50, 50, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 2, 2, 2, 2, 2, 2, 15, 15, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 101 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184328307 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184328307 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184328307/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184328307/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184328307 Building ZINC001184328307 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184328307' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184328307 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184328307 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184328307/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184328307 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 178) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/178: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)N1CCC2(CN(C(=O)OC(C)(C)C)c3ccc(Cl)cc32)CC1) `ZINC001184328307.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184328307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184328307/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184328307 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CCC2(CN(C(=O)OC(C)(C)C)c3ccc(Cl)cc32)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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 3, 7, 13, 13, 13, 13, 13, 13, 28, 28, 49, 49, 49, 49, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13, 13, 13, 49, 49, 49, 49, 49, 49, 49, 49, 49, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184328307 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184328307/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184328307 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 179) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/179: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)N1CCC2(CN(C(=O)OC(C)(C)C)c3ccc(Cl)cc32)CC1) `ZINC001184328307.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184328307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184328307/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184328307 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CCC2(CN(C(=O)OC(C)(C)C)c3ccc(Cl)cc32)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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 5, 12, 15, 15, 15, 15, 15, 15, 26, 26, 50, 50, 50, 50, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 2, 2, 2, 2, 2, 2, 15, 15, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 101 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184328307 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184328307 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184328307/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184328307/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184328307 Building ZINC001184329824 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184329824' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184329824 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184329824 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184329824/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184329824 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 180) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/180 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/180' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1CN(CCc1cc(OC)c(Cl)cc1OC)C(=O)[C@]([O-])([SiH3])CC(C)C) `ZINC001184329824.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184329824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184329824/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184329824 none COc1ccccc1CN(CCc1cc(OC)c(Cl)cc1OC)C(=O)[C@]([O-])([SiH3])CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 5, 5, 1, 1, 1, 12, 5, 1, 16, 1, 1, 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, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 4, 4, 4, 4, 4, 4, 4, 3, 4, 7, 7, 25, 25, 25, 50, 25, 25, 25, 25, 25, 42, 1, 3, 1, 1, 1, 2, 2, 2, 7, 7, 7, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 25, 50, 50, 50, 25, 42, 42, 42, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [25, 26, 27, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 133 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184329824 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184329824/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184329824 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 181) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/181 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/181' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1CN(CCc1cc(OC)c(Cl)cc1OC)C(=O)[C@@]([O-])([SiH3])CC(C)C) `ZINC001184329824.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184329824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184329824/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184329824 none COc1ccccc1CN(CCc1cc(OC)c(Cl)cc1OC)C(=O)[C@@]([O-])([SiH3])CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 5, 5, 1, 1, 1, 12, 5, 1, 16, 1, 1, 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, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 3, 3, 3, 3, 3, 3, 2, 1, 2, 5, 5, 26, 26, 26, 47, 26, 26, 26, 26, 26, 43, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 26, 47, 47, 47, 26, 43, 43, 43, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [59, 9, 57, 55, 60, 56, 58, 52, 53, 54, 23, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 122 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184329824 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184329824 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184329824/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184329824/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184329824 Building ZINC001184329824 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184329824' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184329824 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184329824 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184329824/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184329824 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 180) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/180: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1CN(CCc1cc(OC)c(Cl)cc1OC)C(=O)[C@]([O-])([SiH3])CC(C)C) `ZINC001184329824.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184329824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184329824/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184329824 none COc1ccccc1CN(CCc1cc(OC)c(Cl)cc1OC)C(=O)[C@]([O-])([SiH3])CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 5, 5, 1, 1, 1, 12, 5, 1, 16, 1, 1, 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, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 4, 4, 4, 4, 4, 4, 4, 3, 4, 7, 7, 25, 25, 25, 50, 25, 25, 25, 25, 25, 42, 1, 3, 1, 1, 1, 2, 2, 2, 7, 7, 7, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 25, 50, 50, 50, 25, 42, 42, 42, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [25, 26, 27, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 133 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184329824 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184329824/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184329824 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 181) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/181: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1CN(CCc1cc(OC)c(Cl)cc1OC)C(=O)[C@@]([O-])([SiH3])CC(C)C) `ZINC001184329824.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184329824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184329824/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184329824 none COc1ccccc1CN(CCc1cc(OC)c(Cl)cc1OC)C(=O)[C@@]([O-])([SiH3])CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 5, 5, 1, 1, 1, 12, 5, 1, 16, 1, 1, 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, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 3, 3, 3, 3, 3, 3, 2, 1, 2, 5, 5, 26, 26, 26, 47, 26, 26, 26, 26, 26, 43, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 26, 47, 47, 47, 26, 43, 43, 43, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [59, 9, 57, 55, 60, 56, 58, 52, 53, 54, 23, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 122 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184329824 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184329824 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184329824/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184329824/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184329824 Building ZINC001184330447 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184330447' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184330447 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184330447 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184330447/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184330447 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 182) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/182 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/182' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(CN(C(=O)[C@]([O-])([SiH3])CC(C)C)[C@H]2CC[C@H](NC(=O)OC(C)(C)C)CC2)cc1) `ZINC001184330447.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184330447.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184330447/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC001184330447 none Cc1ccc(CN(C(=O)[C@]([O-])([SiH3])CC(C)C)[C@H]2CC[C@H](NC(=O)OC(C)(C)C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 7, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 6, 6, 6, 6, 6, 6, 17, 26, 26, 41, 43, 43, 43, 6, 6, 9, 9, 9, 9, 9, 9, 9, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 17, 43, 43, 43, 43, 43, 43, 43, 43, 43, 6, 6, 6, 6, 9, 9] 50 rigid atoms, others: [45, 43, 7, 40, 9, 10, 11, 12, 13, 14, 44, 48, 46, 41, 47, 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, 37, 38, 39, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 145 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184330447 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184330447/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184330447 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 183) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/183 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/183' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(CN(C(=O)[C@@]([O-])([SiH3])CC(C)C)[C@H]2CC[C@H](NC(=O)OC(C)(C)C)CC2)cc1) `ZINC001184330447.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184330447.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184330447/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC001184330447 none Cc1ccc(CN(C(=O)[C@@]([O-])([SiH3])CC(C)C)[C@H]2CC[C@H](NC(=O)OC(C)(C)C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 7, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 11, 16, 16, 31, 31, 31, 31, 3, 3, 8, 8, 8, 8, 8, 8, 8, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 11, 31, 31, 31, 31, 31, 31, 31, 31, 31, 3, 3, 3, 3, 8, 8] 50 rigid atoms, others: [45, 43, 6, 7, 8, 9, 10, 11, 12, 13, 14, 44, 48, 40, 46, 41, 47, 42] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 102 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184330447 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184330447 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184330447/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184330447/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184330447 Building ZINC001184330447 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184330447' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184330447 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184330447 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184330447/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184330447 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 182) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/182: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(CN(C(=O)[C@]([O-])([SiH3])CC(C)C)[C@H]2CC[C@H](NC(=O)OC(C)(C)C)CC2)cc1) `ZINC001184330447.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184330447.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184330447/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC001184330447 none Cc1ccc(CN(C(=O)[C@]([O-])([SiH3])CC(C)C)[C@H]2CC[C@H](NC(=O)OC(C)(C)C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 7, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 6, 6, 6, 6, 6, 6, 17, 26, 26, 41, 43, 43, 43, 6, 6, 9, 9, 9, 9, 9, 9, 9, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 17, 43, 43, 43, 43, 43, 43, 43, 43, 43, 6, 6, 6, 6, 9, 9] 50 rigid atoms, others: [45, 43, 7, 40, 9, 10, 11, 12, 13, 14, 44, 48, 46, 41, 47, 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, 37, 38, 39, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 145 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184330447 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184330447/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184330447 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 183) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/183: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(CN(C(=O)[C@@]([O-])([SiH3])CC(C)C)[C@H]2CC[C@H](NC(=O)OC(C)(C)C)CC2)cc1) `ZINC001184330447.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184330447.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184330447/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC001184330447 none Cc1ccc(CN(C(=O)[C@@]([O-])([SiH3])CC(C)C)[C@H]2CC[C@H](NC(=O)OC(C)(C)C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 7, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 11, 16, 16, 31, 31, 31, 31, 3, 3, 8, 8, 8, 8, 8, 8, 8, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 11, 31, 31, 31, 31, 31, 31, 31, 31, 31, 3, 3, 3, 3, 8, 8] 50 rigid atoms, others: [45, 43, 6, 7, 8, 9, 10, 11, 12, 13, 14, 44, 48, 40, 46, 41, 47, 42] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 102 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184330447 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184330447 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184330447/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184330447/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184330447 Building ZINC001184331979 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184331979' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184331979 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184331979 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184331979/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184331979 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 184) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/184 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/184' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@@]([O-])([SiH3])CC(C)C)ccc1C(=O)N1CCCC(=O)c2cc(Cl)ccc21) `ZINC001184331979.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184331979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184331979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184331979 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])CC(C)C)ccc1C(=O)N1CCCC(=O)c2cc(Cl)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', '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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 1, 11, 1, 1, 1, 16, 1, 1, 1, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 16, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 44, 40, 3, 43, 41, 36, 38, 42, 39, 37] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184331979 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184331979/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184331979 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 185) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/185 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/185' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@]([O-])([SiH3])CC(C)C)ccc1C(=O)N1CCCC(=O)c2cc(Cl)ccc21) `ZINC001184331979.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184331979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184331979/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184331979 none Cc1cc(NC(=O)[C@]([O-])([SiH3])CC(C)C)ccc1C(=O)N1CCCC(=O)c2cc(Cl)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', '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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 1, 11, 1, 1, 1, 16, 1, 1, 1, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 1, 3, 30, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 44, 40, 3, 43, 41, 36, 38, 42, 39, 37] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184331979 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184331979 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184331979/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184331979/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184331979 Building ZINC001184331979 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184331979' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184331979 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184331979 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184331979/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184331979 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 184) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/184: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@@]([O-])([SiH3])CC(C)C)ccc1C(=O)N1CCCC(=O)c2cc(Cl)ccc21) `ZINC001184331979.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184331979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184331979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184331979 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])CC(C)C)ccc1C(=O)N1CCCC(=O)c2cc(Cl)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', '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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 1, 11, 1, 1, 1, 16, 1, 1, 1, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 16, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 44, 40, 3, 43, 41, 36, 38, 42, 39, 37] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184331979 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184331979/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184331979 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 185) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/185: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@]([O-])([SiH3])CC(C)C)ccc1C(=O)N1CCCC(=O)c2cc(Cl)ccc21) `ZINC001184331979.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184331979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184331979/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184331979 none Cc1cc(NC(=O)[C@]([O-])([SiH3])CC(C)C)ccc1C(=O)N1CCCC(=O)c2cc(Cl)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', '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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 1, 11, 1, 1, 1, 16, 1, 1, 1, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 1, 3, 30, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 44, 40, 3, 43, 41, 36, 38, 42, 39, 37] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184331979 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184331979 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184331979/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184331979/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184331979 Building ZINC001184488315 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488315' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488315 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184488315 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488315/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488315 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 186) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/186 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/186' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(C2CCOCC2)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184488315.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184488315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488315/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001184488315 none O=C(Nc1ccc(C2CCOCC2)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 5, 5, 12, 5, 5, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 10, 10, 4, 5, 26, 26, 28, 28, 26, 10, 10, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 10, 10, 26, 26, 26, 28, 28, 28, 28, 26, 26, 10, 10, 9, 9, 9, 9] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488315 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488315/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488315 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 187) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/187 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/187' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(C2CCOCC2)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184488315.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184488315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488315/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001184488315 none O=C(Nc1ccc(C2CCOCC2)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 5, 5, 12, 5, 5, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 9, 6, 11, 30, 30, 30, 30, 30, 9, 9, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 9, 9, 30, 30, 30, 30, 30, 30, 30, 30, 30, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488315 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184488315 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488315/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488315/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488315 Building ZINC001184488315 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488315' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488315 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184488315 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488315/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488315 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 186) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/186: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(C2CCOCC2)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184488315.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184488315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488315/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001184488315 none O=C(Nc1ccc(C2CCOCC2)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 5, 5, 12, 5, 5, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 10, 10, 4, 5, 26, 26, 28, 28, 26, 10, 10, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 10, 10, 26, 26, 26, 28, 28, 28, 28, 26, 26, 10, 10, 9, 9, 9, 9] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488315 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488315/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488315 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 187) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/187: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(C2CCOCC2)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184488315.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184488315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488315/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001184488315 none O=C(Nc1ccc(C2CCOCC2)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 5, 5, 12, 5, 5, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 9, 6, 11, 30, 30, 30, 30, 30, 9, 9, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 9, 9, 30, 30, 30, 30, 30, 30, 30, 30, 30, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488315 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184488315 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488315/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488315/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488315 Building ZINC001184488524 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488524' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488524 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184488524 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488524/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488524 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 188) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/188 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/188' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(OC(F)(F)F)c1F)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184488524.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184488524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488524/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001184488524 none O=C(Nc1cccc(OC(F)(F)F)c1F)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 6, 6, 6, 28, 28, 28, 28, 6, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 6, 6, 6, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488524 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488524/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488524 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 189) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/189 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/189' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(OC(F)(F)F)c1F)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184488524.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184488524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488524/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001184488524 none O=C(Nc1cccc(OC(F)(F)F)c1F)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 6, 6, 6, 28, 28, 28, 28, 6, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 6, 6, 6, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488524 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184488524 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488524/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488524/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488524 Building ZINC001184488524 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488524' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488524 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184488524 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488524/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488524 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 188) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/188: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(OC(F)(F)F)c1F)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184488524.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184488524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488524/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001184488524 none O=C(Nc1cccc(OC(F)(F)F)c1F)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 6, 6, 6, 28, 28, 28, 28, 6, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 6, 6, 6, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488524 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488524/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488524 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 189) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/189: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(OC(F)(F)F)c1F)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184488524.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184488524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488524/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001184488524 none O=C(Nc1cccc(OC(F)(F)F)c1F)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 6, 6, 6, 28, 28, 28, 28, 6, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 6, 6, 6, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488524 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184488524 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488524/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488524/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488524 Building ZINC001184488953 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488953' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488953 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184488953 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488953/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488953 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 190) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/190 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/190' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@H](C(=O)c1ccccc1)N(C)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184488953.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184488953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488953/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184488953 none CCC[C@@H](C(=O)c1ccccc1)N(C)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 7, 4, 7, 7, 13, 13, 16, 16, 13, 16, 16, 2, 4, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13, 13, 13, 13, 13, 13, 16, 16, 15, 16, 16, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488953 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488953/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488953 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 191) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/191 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/191' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@H](C(=O)c1ccccc1)N(C)C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184488953.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184488953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488953/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184488953 none CCC[C@@H](C(=O)c1ccccc1)N(C)C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 6, 4, 6, 6, 14, 14, 20, 20, 16, 20, 20, 2, 4, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 20, 20, 17, 20, 20, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488953 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184488953 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488953/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488953/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488953 Building ZINC001184488953 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488953' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488953 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184488953 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488953/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488953 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 190) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/190: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@H](C(=O)c1ccccc1)N(C)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184488953.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184488953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488953/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184488953 none CCC[C@@H](C(=O)c1ccccc1)N(C)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 7, 4, 7, 7, 13, 13, 16, 16, 13, 16, 16, 2, 4, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13, 13, 13, 13, 13, 13, 16, 16, 15, 16, 16, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488953 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488953/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488953 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 191) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/191: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@H](C(=O)c1ccccc1)N(C)C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184488953.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184488953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488953/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184488953 none CCC[C@@H](C(=O)c1ccccc1)N(C)C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 6, 4, 6, 6, 14, 14, 20, 20, 16, 20, 20, 2, 4, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 20, 20, 17, 20, 20, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488953 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184488953 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488953/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488953/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488953 Building ZINC001184488954 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488954' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488954 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184488954 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488954/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488954 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 192) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/192 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/192' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@H](C(=O)c1ccccc1)N(C)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184488954.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184488954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488954/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184488954 none CCC[C@H](C(=O)c1ccccc1)N(C)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 6, 4, 6, 6, 14, 14, 20, 20, 18, 20, 20, 2, 4, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 20, 20, 19, 20, 20, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488954 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488954/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488954 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 193) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/193 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/193' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@H](C(=O)c1ccccc1)N(C)C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184488954.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184488954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488954/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184488954 none CCC[C@H](C(=O)c1ccccc1)N(C)C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 7, 4, 7, 7, 13, 13, 17, 17, 13, 17, 17, 2, 4, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13, 13, 13, 13, 13, 13, 17, 17, 16, 17, 17, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488954 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184488954 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488954/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488954/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488954 Building ZINC001184488954 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488954' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488954 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184488954 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488954/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488954 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 192) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/192: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@H](C(=O)c1ccccc1)N(C)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184488954.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184488954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488954/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184488954 none CCC[C@H](C(=O)c1ccccc1)N(C)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 6, 4, 6, 6, 14, 14, 20, 20, 18, 20, 20, 2, 4, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 20, 20, 19, 20, 20, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488954 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488954/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488954 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 193) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/193: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@H](C(=O)c1ccccc1)N(C)C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184488954.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184488954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488954/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184488954 none CCC[C@H](C(=O)c1ccccc1)N(C)C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 7, 4, 7, 7, 13, 13, 17, 17, 13, 17, 17, 2, 4, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13, 13, 13, 13, 13, 13, 17, 17, 16, 17, 17, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488954 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184488954 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488954/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488954/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184488954 Building ZINC001184489277 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489277' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489277 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489277 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489277/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489277 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 194) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/194 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/194' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(C(C)(C)c4ccc(N)cc4)cc3)c2c1) `ZINC001184489277.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489277/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184489277 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(C(C)(C)c4ccc(N)cc4)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 5, 5, 4, 5, 31, 31, 31, 32, 32, 31, 31, 32, 32, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 3, 5, 5, 31, 31, 31, 31, 31, 31, 32, 32, 32, 32, 32, 32, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489277 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489277/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489277 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 195) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/195 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/195' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(C(C)(C)c4ccc(N)cc4)cc3)c2c1) `ZINC001184489277.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489277/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184489277 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(C(C)(C)c4ccc(N)cc4)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 5, 5, 3, 3, 28, 29, 27, 31, 31, 30, 30, 31, 31, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 3, 5, 5, 30, 29, 27, 30, 26, 29, 31, 31, 31, 31, 31, 31, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489277 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184489277 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489277/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489277/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489277 Building ZINC001184489277 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489277' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489277 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489277 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489277/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489277 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 194) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/194: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(C(C)(C)c4ccc(N)cc4)cc3)c2c1) `ZINC001184489277.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489277/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184489277 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(C(C)(C)c4ccc(N)cc4)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 5, 5, 4, 5, 31, 31, 31, 32, 32, 31, 31, 32, 32, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 3, 5, 5, 31, 31, 31, 31, 31, 31, 32, 32, 32, 32, 32, 32, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489277 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489277/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489277 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 195) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/195: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(C(C)(C)c4ccc(N)cc4)cc3)c2c1) `ZINC001184489277.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489277/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184489277 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(C(C)(C)c4ccc(N)cc4)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 5, 5, 3, 3, 28, 29, 27, 31, 31, 30, 30, 31, 31, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 3, 5, 5, 30, 29, 27, 30, 26, 29, 31, 31, 31, 31, 31, 31, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489277 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184489277 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489277/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489277/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489277 Building ZINC001184489345 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489345' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489345 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489345 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489345/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489345 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 196) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/196 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/196' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3c(Cl)cccc3NC(=O)OC(C)(C)C)c2c1) `ZINC001184489345.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489345/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489345 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3c(Cl)cccc3NC(=O)OC(C)(C)C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 16, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 6, 7, 7, 7, 13, 17, 17, 24, 25, 25, 25, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 13, 25, 25, 25, 25, 25, 25, 25, 25, 25, 7] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489345 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489345/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489345 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 197) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/197 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/197' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3c(Cl)cccc3NC(=O)OC(C)(C)C)c2c1) `ZINC001184489345.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489345/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489345 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3c(Cl)cccc3NC(=O)OC(C)(C)C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 16, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 6, 7, 7, 7, 14, 18, 18, 25, 26, 26, 26, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 14, 26, 26, 26, 26, 26, 26, 26, 26, 26, 7] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489345 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184489345 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489345/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489345/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489345 Building ZINC001184489345 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489345' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489345 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489345 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489345/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489345 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 196) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/196: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3c(Cl)cccc3NC(=O)OC(C)(C)C)c2c1) `ZINC001184489345.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489345/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489345 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3c(Cl)cccc3NC(=O)OC(C)(C)C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 16, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 6, 7, 7, 7, 13, 17, 17, 24, 25, 25, 25, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 13, 25, 25, 25, 25, 25, 25, 25, 25, 25, 7] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489345 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489345/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489345 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 197) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/197: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3c(Cl)cccc3NC(=O)OC(C)(C)C)c2c1) `ZINC001184489345.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489345/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489345 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3c(Cl)cccc3NC(=O)OC(C)(C)C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 16, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 6, 7, 7, 7, 14, 18, 18, 25, 26, 26, 26, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 14, 26, 26, 26, 26, 26, 26, 26, 26, 26, 7] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489345 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184489345 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489345/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489345/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489345 Building ZINC001184489346 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184489346 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 198) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/198 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/198' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc4c(c3)CN(Cc3ccccc3)C4)c2c1) `ZINC001184489346.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184489346 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc4c(c3)CN(Cc3ccccc3)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 11, 11, 20, 20, 8, 20, 20, 20, 36, 36, 36, 36, 36, 36, 20, 4, 4, 4, 4, 4, 4, 4, 4, 3, 11, 20, 16, 20, 20, 36, 36, 36, 36, 36, 36, 36, 20, 20, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 199) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/199 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/199' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc4c(c3)CN(Cc3ccccc3)C4)c2c1) `ZINC001184489346.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184489346 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc4c(c3)CN(Cc3ccccc3)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 11, 11, 20, 20, 8, 20, 20, 20, 36, 36, 36, 36, 36, 36, 20, 4, 4, 4, 4, 4, 4, 4, 4, 3, 11, 20, 16, 20, 20, 36, 36, 36, 36, 36, 36, 36, 20, 20, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 200) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/200 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/200' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc4c(c3)CN(Cc3ccccc3)C4)c2c1) `ZINC001184489346.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184489346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184489346 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc4c(c3)CN(Cc3ccccc3)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 11, 11, 20, 20, 8, 20, 20, 20, 36, 36, 36, 36, 36, 36, 20, 4, 4, 4, 4, 4, 4, 4, 4, 3, 11, 20, 16, 20, 20, 36, 36, 36, 36, 36, 36, 36, 20, 20, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 201) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/201 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/201' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc4c(c3)CN(Cc3ccccc3)C4)c2c1) `ZINC001184489346.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184489346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184489346 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc4c(c3)CN(Cc3ccccc3)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 11, 11, 20, 20, 8, 20, 20, 20, 36, 36, 36, 36, 36, 36, 20, 4, 4, 4, 4, 4, 4, 4, 4, 3, 11, 20, 16, 20, 20, 36, 36, 36, 36, 36, 36, 36, 20, 20, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184489346 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346 Building ZINC001184489346 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184489346 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 198) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/198: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc4c(c3)CN(Cc3ccccc3)C4)c2c1) `ZINC001184489346.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184489346 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc4c(c3)CN(Cc3ccccc3)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 11, 11, 20, 20, 8, 20, 20, 20, 36, 36, 36, 36, 36, 36, 20, 4, 4, 4, 4, 4, 4, 4, 4, 3, 11, 20, 16, 20, 20, 36, 36, 36, 36, 36, 36, 36, 20, 20, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 199) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/199: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc4c(c3)CN(Cc3ccccc3)C4)c2c1) `ZINC001184489346.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184489346 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc4c(c3)CN(Cc3ccccc3)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 11, 11, 20, 20, 8, 20, 20, 20, 36, 36, 36, 36, 36, 36, 20, 4, 4, 4, 4, 4, 4, 4, 4, 3, 11, 20, 16, 20, 20, 36, 36, 36, 36, 36, 36, 36, 20, 20, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 200) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/200: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc4c(c3)CN(Cc3ccccc3)C4)c2c1) `ZINC001184489346.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184489346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184489346 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc4c(c3)CN(Cc3ccccc3)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 11, 11, 20, 20, 8, 20, 20, 20, 36, 36, 36, 36, 36, 36, 20, 4, 4, 4, 4, 4, 4, 4, 4, 3, 11, 20, 16, 20, 20, 36, 36, 36, 36, 36, 36, 36, 20, 20, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 201) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/201: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc4c(c3)CN(Cc3ccccc3)C4)c2c1) `ZINC001184489346.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184489346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184489346 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc4c(c3)CN(Cc3ccccc3)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 11, 11, 20, 20, 8, 20, 20, 20, 36, 36, 36, 36, 36, 36, 20, 4, 4, 4, 4, 4, 4, 4, 4, 3, 11, 20, 16, 20, 20, 36, 36, 36, 36, 36, 36, 36, 20, 20, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184489346 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346 Building ZINC001184489346 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184489346 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 198) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/198: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc4c(c3)CN(Cc3ccccc3)C4)c2c1) `ZINC001184489346.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184489346 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc4c(c3)CN(Cc3ccccc3)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 11, 11, 20, 20, 8, 20, 20, 20, 36, 36, 36, 36, 36, 36, 20, 4, 4, 4, 4, 4, 4, 4, 4, 3, 11, 20, 16, 20, 20, 36, 36, 36, 36, 36, 36, 36, 20, 20, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 199) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/199: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc4c(c3)CN(Cc3ccccc3)C4)c2c1) `ZINC001184489346.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184489346 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc4c(c3)CN(Cc3ccccc3)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 11, 11, 20, 20, 8, 20, 20, 20, 36, 36, 36, 36, 36, 36, 20, 4, 4, 4, 4, 4, 4, 4, 4, 3, 11, 20, 16, 20, 20, 36, 36, 36, 36, 36, 36, 36, 20, 20, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 200) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/200: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc4c(c3)CN(Cc3ccccc3)C4)c2c1) `ZINC001184489346.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184489346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184489346 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc4c(c3)CN(Cc3ccccc3)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 11, 11, 20, 20, 8, 20, 20, 20, 36, 36, 36, 36, 36, 36, 20, 4, 4, 4, 4, 4, 4, 4, 4, 3, 11, 20, 16, 20, 20, 36, 36, 36, 36, 36, 36, 36, 20, 20, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 201) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/201: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc4c(c3)CN(Cc3ccccc3)C4)c2c1) `ZINC001184489346.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184489346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184489346 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc4c(c3)CN(Cc3ccccc3)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 11, 11, 20, 20, 8, 20, 20, 20, 36, 36, 36, 36, 36, 36, 20, 4, 4, 4, 4, 4, 4, 4, 4, 3, 11, 20, 16, 20, 20, 36, 36, 36, 36, 36, 36, 36, 20, 20, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184489346 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346 Building ZINC001184489346 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184489346 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 198) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/198: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc4c(c3)CN(Cc3ccccc3)C4)c2c1) `ZINC001184489346.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184489346 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc4c(c3)CN(Cc3ccccc3)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 11, 11, 20, 20, 8, 20, 20, 20, 36, 36, 36, 36, 36, 36, 20, 4, 4, 4, 4, 4, 4, 4, 4, 3, 11, 20, 16, 20, 20, 36, 36, 36, 36, 36, 36, 36, 20, 20, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 199) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/199: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc4c(c3)CN(Cc3ccccc3)C4)c2c1) `ZINC001184489346.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184489346 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc4c(c3)CN(Cc3ccccc3)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 11, 11, 20, 20, 8, 20, 20, 20, 36, 36, 36, 36, 36, 36, 20, 4, 4, 4, 4, 4, 4, 4, 4, 3, 11, 20, 16, 20, 20, 36, 36, 36, 36, 36, 36, 36, 20, 20, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 200) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/200: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc4c(c3)CN(Cc3ccccc3)C4)c2c1) `ZINC001184489346.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184489346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184489346 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc4c(c3)CN(Cc3ccccc3)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 11, 11, 20, 20, 8, 20, 20, 20, 36, 36, 36, 36, 36, 36, 20, 4, 4, 4, 4, 4, 4, 4, 4, 3, 11, 20, 16, 20, 20, 36, 36, 36, 36, 36, 36, 36, 20, 20, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 201) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/201: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc4c(c3)CN(Cc3ccccc3)C4)c2c1) `ZINC001184489346.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184489346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184489346 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc4c(c3)CN(Cc3ccccc3)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 11, 11, 20, 20, 8, 20, 20, 20, 36, 36, 36, 36, 36, 36, 20, 4, 4, 4, 4, 4, 4, 4, 4, 3, 11, 20, 16, 20, 20, 36, 36, 36, 36, 36, 36, 36, 20, 20, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184489346 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489346 Building ZINC001184489635 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489635' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489635 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489635 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489635/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489635 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 202) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/202 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/202' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC(c4ccc(OC(F)(F)F)cc4)CC3)c2c1) `ZINC001184489635.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489635/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489635 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC(c4ccc(OC(F)(F)F)cc4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 4, 6, 7, 7, 7, 7, 10, 10, 7, 9, 38, 38, 38, 38, 10, 10, 7, 7, 4, 4, 5, 5, 5, 4, 4, 4, 7, 7, 7, 7, 7, 10, 10, 10, 10, 7, 7, 7, 7, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489635 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489635/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489635 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 203) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/203 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/203' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC(c4ccc(OC(F)(F)F)cc4)CC3)c2c1) `ZINC001184489635.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489635/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489635 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC(c4ccc(OC(F)(F)F)cc4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 5, 5, 5, 5, 5, 9, 9, 5, 7, 30, 29, 30, 30, 9, 9, 5, 5, 4, 4, 5, 5, 5, 4, 4, 4, 5, 5, 5, 5, 5, 9, 9, 9, 9, 5, 5, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489635 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184489635 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489635/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489635/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489635 Building ZINC001184489635 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489635' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489635 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489635 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489635/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489635 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 202) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/202: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC(c4ccc(OC(F)(F)F)cc4)CC3)c2c1) `ZINC001184489635.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489635/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489635 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC(c4ccc(OC(F)(F)F)cc4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 4, 6, 7, 7, 7, 7, 10, 10, 7, 9, 38, 38, 38, 38, 10, 10, 7, 7, 4, 4, 5, 5, 5, 4, 4, 4, 7, 7, 7, 7, 7, 10, 10, 10, 10, 7, 7, 7, 7, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489635 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489635/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489635 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 203) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/203: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC(c4ccc(OC(F)(F)F)cc4)CC3)c2c1) `ZINC001184489635.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489635/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489635 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC(c4ccc(OC(F)(F)F)cc4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 5, 5, 5, 5, 5, 9, 9, 5, 7, 30, 29, 30, 30, 9, 9, 5, 5, 4, 4, 5, 5, 5, 4, 4, 4, 5, 5, 5, 5, 5, 9, 9, 9, 9, 5, 5, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489635 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184489635 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489635/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489635/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489635 Building ZINC001184489685 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489685' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489685 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489685 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489685/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489685 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 204) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/204 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/204' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(Sc4nc(C)cc(C)n4)cc3)c2c1) `ZINC001184489685.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489685/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489685 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(Sc4nc(C)cc(C)n4)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 1, 8, 1, 5, 1, 1, 5, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 4, 4, 3, 4, 19, 34, 34, 34, 21, 34, 34, 34, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 34, 34, 34, 21, 34, 34, 34, 4, 4, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489685 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489685/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489685 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 205) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/205 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/205' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(Sc4nc(C)cc(C)n4)cc3)c2c1) `ZINC001184489685.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489685/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489685 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(Sc4nc(C)cc(C)n4)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 1, 8, 1, 5, 1, 1, 5, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 4, 4, 4, 4, 21, 33, 33, 33, 21, 33, 33, 33, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 33, 33, 33, 21, 33, 33, 33, 4, 4, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489685 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184489685 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489685/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489685/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489685 Building ZINC001184489685 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489685' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489685 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489685 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489685/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489685 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 204) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/204: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(Sc4nc(C)cc(C)n4)cc3)c2c1) `ZINC001184489685.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489685/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489685 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(Sc4nc(C)cc(C)n4)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 1, 8, 1, 5, 1, 1, 5, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 4, 4, 3, 4, 19, 34, 34, 34, 21, 34, 34, 34, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 34, 34, 34, 21, 34, 34, 34, 4, 4, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489685 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489685/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489685 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 205) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/205: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(Sc4nc(C)cc(C)n4)cc3)c2c1) `ZINC001184489685.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489685/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489685 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(Sc4nc(C)cc(C)n4)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 1, 8, 1, 5, 1, 1, 5, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 4, 4, 4, 4, 21, 33, 33, 33, 21, 33, 33, 33, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 33, 33, 33, 21, 33, 33, 33, 4, 4, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489685 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184489685 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489685/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489685/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489685 Building ZINC001184489809 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489809' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489809 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489809 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489809/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489809 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 206) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/206 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/206' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@H]3c3ccc(OC(F)(F)F)cc3)c2c1) `ZINC001184489809.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184489809 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@H]3c3ccc(OC(F)(F)F)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 6, 6, 3, 3, 20, 20, 20, 20, 6, 6, 3, 3, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489809 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489809/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489809 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 207) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/207 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/207' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@H]3c3ccc(OC(F)(F)F)cc3)c2c1) `ZINC001184489809.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489809/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184489809 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@H]3c3ccc(OC(F)(F)F)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 11, 11, 6, 6, 34, 40, 40, 40, 11, 11, 3, 3, 5, 5, 5, 3, 3, 3, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489809 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184489809 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489809/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489809/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489809 Building ZINC001184489809 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489809' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489809 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489809 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489809/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489809 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 206) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/206: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@H]3c3ccc(OC(F)(F)F)cc3)c2c1) `ZINC001184489809.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184489809 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@H]3c3ccc(OC(F)(F)F)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 6, 6, 3, 3, 20, 20, 20, 20, 6, 6, 3, 3, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489809 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489809/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489809 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 207) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/207: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@H]3c3ccc(OC(F)(F)F)cc3)c2c1) `ZINC001184489809.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489809/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184489809 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@H]3c3ccc(OC(F)(F)F)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 11, 11, 6, 6, 34, 40, 40, 40, 11, 11, 3, 3, 5, 5, 5, 3, 3, 3, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489809 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184489809 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489809/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489809/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489809 Building ZINC001184489811 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489811' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489811 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489811 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489811/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489811 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 208) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/208 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/208' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@@H]3c3ccc(OC(F)(F)F)cc3)c2c1) `ZINC001184489811.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489811/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184489811 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@@H]3c3ccc(OC(F)(F)F)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 10, 10, 6, 6, 34, 40, 40, 40, 10, 10, 3, 3, 5, 5, 5, 3, 3, 3, 6, 6, 6, 6, 6, 6, 10, 10, 10, 10, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489811 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489811/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489811 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 209) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/209 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/209' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@@H]3c3ccc(OC(F)(F)F)cc3)c2c1) `ZINC001184489811.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489811/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184489811 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@@H]3c3ccc(OC(F)(F)F)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 6, 6, 4, 4, 21, 21, 21, 21, 6, 6, 3, 3, 4, 4, 4, 3, 3, 3, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489811 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184489811 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489811/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489811/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489811 Building ZINC001184489811 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489811' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489811 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489811 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489811/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489811 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 208) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/208: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@@H]3c3ccc(OC(F)(F)F)cc3)c2c1) `ZINC001184489811.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489811/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184489811 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@@H]3c3ccc(OC(F)(F)F)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 10, 10, 6, 6, 34, 40, 40, 40, 10, 10, 3, 3, 5, 5, 5, 3, 3, 3, 6, 6, 6, 6, 6, 6, 10, 10, 10, 10, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489811 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489811/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489811 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 209) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/209: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@@H]3c3ccc(OC(F)(F)F)cc3)c2c1) `ZINC001184489811.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489811/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184489811 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@@H]3c3ccc(OC(F)(F)F)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 6, 6, 4, 4, 21, 21, 21, 21, 6, 6, 3, 3, 4, 4, 4, 3, 3, 3, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489811 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184489811 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489811/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489811/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489811 Building ZINC001184489931 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489931' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489931 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489931 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489931/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489931 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 210) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/210 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/210' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc4c(c3)N(C(=O)OC(C)(C)C)CCC4)c2c1) `ZINC001184489931.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489931/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184489931 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc4c(c3)N(C(=O)OC(C)(C)C)CCC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 13, 25, 25, 25, 21, 25, 25, 26, 26, 26, 26, 26, 26, 25, 25, 25, 4, 4, 4, 4, 4, 4, 4, 4, 3, 25, 25, 25, 26, 26, 26, 26, 26, 26, 26, 26, 26, 25, 25, 25, 25, 25, 25, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489931 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489931/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489931 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 211) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/211 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/211' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc4c(c3)N(C(=O)OC(C)(C)C)CCC4)c2c1) `ZINC001184489931.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489931/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184489931 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc4c(c3)N(C(=O)OC(C)(C)C)CCC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 12, 21, 21, 21, 18, 21, 21, 24, 24, 24, 24, 24, 24, 21, 21, 21, 4, 4, 4, 4, 4, 4, 4, 4, 3, 21, 21, 21, 24, 24, 24, 24, 24, 24, 24, 24, 24, 21, 21, 21, 21, 21, 21, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489931 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184489931 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489931/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489931/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489931 Building ZINC001184489931 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489931' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489931 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489931 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489931/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489931 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 210) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/210: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc4c(c3)N(C(=O)OC(C)(C)C)CCC4)c2c1) `ZINC001184489931.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489931/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184489931 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc4c(c3)N(C(=O)OC(C)(C)C)CCC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 13, 25, 25, 25, 21, 25, 25, 26, 26, 26, 26, 26, 26, 25, 25, 25, 4, 4, 4, 4, 4, 4, 4, 4, 3, 25, 25, 25, 26, 26, 26, 26, 26, 26, 26, 26, 26, 25, 25, 25, 25, 25, 25, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489931 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489931/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489931 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 211) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/211: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc4c(c3)N(C(=O)OC(C)(C)C)CCC4)c2c1) `ZINC001184489931.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489931/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184489931 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc4c(c3)N(C(=O)OC(C)(C)C)CCC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 12, 21, 21, 21, 18, 21, 21, 24, 24, 24, 24, 24, 24, 21, 21, 21, 4, 4, 4, 4, 4, 4, 4, 4, 3, 21, 21, 21, 24, 24, 24, 24, 24, 24, 24, 24, 24, 21, 21, 21, 21, 21, 21, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489931 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184489931 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489931/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489931/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489931 Building ZINC001184489941 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489941' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489941 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489941 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489941/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489941 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 212) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/212 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/212' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cc(n4cnc(C)c4)cc(C(F)(F)F)c3)c2c1) `ZINC001184489941.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489941/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184489941 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cc(n4cnc(C)c4)cc(C(F)(F)F)c3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 1, 8, 1, 5, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 20, 20, 20, 20, 20, 10, 10, 10, 10, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 3, 10, 20, 20, 20, 20, 20, 10, 10, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489941 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489941/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489941 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 213) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/213 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/213' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cc(n4cnc(C)c4)cc(C(F)(F)F)c3)c2c1) `ZINC001184489941.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489941/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184489941 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cc(n4cnc(C)c4)cc(C(F)(F)F)c3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 1, 8, 1, 5, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 20, 20, 20, 20, 20, 10, 10, 10, 10, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 3, 10, 20, 20, 20, 20, 20, 10, 10, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489941 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184489941 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489941/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489941/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489941 Building ZINC001184489941 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489941' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489941 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489941 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489941/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489941 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 212) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/212: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cc(n4cnc(C)c4)cc(C(F)(F)F)c3)c2c1) `ZINC001184489941.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489941/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184489941 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cc(n4cnc(C)c4)cc(C(F)(F)F)c3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 1, 8, 1, 5, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 20, 20, 20, 20, 20, 10, 10, 10, 10, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 3, 10, 20, 20, 20, 20, 20, 10, 10, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489941 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489941/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489941 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 213) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/213: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cc(n4cnc(C)c4)cc(C(F)(F)F)c3)c2c1) `ZINC001184489941.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489941/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184489941 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cc(n4cnc(C)c4)cc(C(F)(F)F)c3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 1, 8, 1, 5, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 20, 20, 20, 20, 20, 10, 10, 10, 10, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 3, 10, 20, 20, 20, 20, 20, 10, 10, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489941 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184489941 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489941/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489941/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184489941 Building ZINC001184490370 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490370' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490370 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490370 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490370/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490370 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 214) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/214 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/214' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccccc3C(=O)c3cc(C)cc(C)c3)c2c1) `ZINC001184490370.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490370/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184490370 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccccc3C(=O)c3cc(C)cc(C)c3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 5, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 12, 12, 12, 18, 18, 21, 21, 21, 18, 21, 21, 21, 6, 6, 8, 8, 8, 6, 6, 6, 5, 12, 12, 12, 12, 21, 21, 21, 21, 18, 21, 21, 21, 21, 6] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490370 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490370/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490370 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 215) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/215 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/215' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccccc3C(=O)c3cc(C)cc(C)c3)c2c1) `ZINC001184490370.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490370/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184490370 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccccc3C(=O)c3cc(C)cc(C)c3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 5, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 5, 5, 5, 11, 11, 9, 11, 11, 11, 17, 17, 20, 20, 20, 17, 20, 20, 20, 7, 7, 9, 9, 9, 7, 7, 7, 5, 11, 11, 11, 11, 20, 20, 20, 20, 17, 20, 20, 20, 20, 7] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490370 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184490370 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490370/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490370/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490370 Building ZINC001184490370 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490370' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490370 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490370 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490370/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490370 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 214) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/214: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccccc3C(=O)c3cc(C)cc(C)c3)c2c1) `ZINC001184490370.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490370/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184490370 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccccc3C(=O)c3cc(C)cc(C)c3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 5, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 12, 12, 12, 18, 18, 21, 21, 21, 18, 21, 21, 21, 6, 6, 8, 8, 8, 6, 6, 6, 5, 12, 12, 12, 12, 21, 21, 21, 21, 18, 21, 21, 21, 21, 6] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490370 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490370/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490370 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 215) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/215: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccccc3C(=O)c3cc(C)cc(C)c3)c2c1) `ZINC001184490370.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490370/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184490370 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccccc3C(=O)c3cc(C)cc(C)c3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 5, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 5, 5, 5, 11, 11, 9, 11, 11, 11, 17, 17, 20, 20, 20, 17, 20, 20, 20, 7, 7, 9, 9, 9, 7, 7, 7, 5, 11, 11, 11, 11, 20, 20, 20, 20, 17, 20, 20, 20, 20, 7] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490370 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184490370 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490370/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490370/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490370 Building ZINC001184490437 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490437' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490437 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490437 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490437/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490437 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 216) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/216 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/216' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(Oc4ccc(C(C)=O)cc4)cc3)c2c1) `ZINC001184490437.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490437/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184490437 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(Oc4ccc(C(C)=O)cc4)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 5, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 20, 20, 20, 20, 20, 29, 29, 20, 20, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 3, 5, 5, 20, 20, 29, 29, 29, 20, 20, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490437 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490437/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490437 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 217) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/217 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/217' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(Oc4ccc(C(C)=O)cc4)cc3)c2c1) `ZINC001184490437.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490437/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184490437 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(Oc4ccc(C(C)=O)cc4)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 5, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 5, 5, 3, 3, 20, 20, 20, 20, 20, 30, 30, 20, 20, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 3, 5, 5, 20, 20, 30, 30, 30, 20, 20, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490437 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184490437 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490437/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490437/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490437 Building ZINC001184490437 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490437' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490437 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490437 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490437/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490437 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 216) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/216: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(Oc4ccc(C(C)=O)cc4)cc3)c2c1) `ZINC001184490437.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490437/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184490437 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(Oc4ccc(C(C)=O)cc4)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 5, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 20, 20, 20, 20, 20, 29, 29, 20, 20, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 3, 5, 5, 20, 20, 29, 29, 29, 20, 20, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490437 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490437/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490437 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 217) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/217: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(Oc4ccc(C(C)=O)cc4)cc3)c2c1) `ZINC001184490437.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490437/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184490437 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(Oc4ccc(C(C)=O)cc4)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 5, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 5, 5, 3, 3, 20, 20, 20, 20, 20, 30, 30, 20, 20, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 3, 5, 5, 20, 20, 30, 30, 30, 20, 20, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490437 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184490437 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490437/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490437/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490437 Building ZINC001184490576 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490576' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490576 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490576 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490576/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490576 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 218) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/218 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/218' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(Oc4ccn5ccnc5c4)cc3C)c2c1) `ZINC001184490576.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490576 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(Oc4ccn5ccnc5c4)cc3C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 6, 6, 3, 5, 29, 29, 29, 29, 29, 29, 29, 29, 29, 6, 6, 6, 4, 4, 4, 4, 4, 4, 4, 4, 3, 6, 6, 29, 29, 29, 29, 29, 6, 6, 6, 6, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490576 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490576/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490576 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 219) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/219 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/219' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(Oc4ccn5ccnc5c4)cc3C)c2c1) `ZINC001184490576.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490576/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490576 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(Oc4ccn5ccnc5c4)cc3C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 6, 6, 3, 3, 28, 28, 28, 28, 28, 28, 28, 28, 28, 6, 6, 6, 4, 4, 4, 4, 4, 4, 4, 4, 3, 6, 6, 28, 28, 28, 28, 28, 6, 6, 6, 6, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490576 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184490576 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490576/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490576/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490576 Building ZINC001184490576 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490576' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490576 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490576 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490576/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490576 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 218) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/218: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(Oc4ccn5ccnc5c4)cc3C)c2c1) `ZINC001184490576.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490576 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(Oc4ccn5ccnc5c4)cc3C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 6, 6, 3, 5, 29, 29, 29, 29, 29, 29, 29, 29, 29, 6, 6, 6, 4, 4, 4, 4, 4, 4, 4, 4, 3, 6, 6, 29, 29, 29, 29, 29, 6, 6, 6, 6, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490576 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490576/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490576 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 219) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/219: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(Oc4ccn5ccnc5c4)cc3C)c2c1) `ZINC001184490576.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490576/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490576 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(Oc4ccn5ccnc5c4)cc3C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 6, 6, 3, 3, 28, 28, 28, 28, 28, 28, 28, 28, 28, 6, 6, 6, 4, 4, 4, 4, 4, 4, 4, 4, 3, 6, 6, 28, 28, 28, 28, 28, 6, 6, 6, 6, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490576 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184490576 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490576/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490576/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490576 Building ZINC001184490616 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490616' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490616 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490616 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490616/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490616 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 220) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/220 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/220' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc4c(cnn4Cc4cccc(F)c4)c3)c2c1) `ZINC001184490616.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490616/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184490616 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc4c(cnn4Cc4cccc(F)c4)c3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 20, 32, 32, 32, 32, 32, 32, 9, 4, 4, 4, 4, 4, 4, 4, 4, 3, 9, 9, 9, 20, 20, 32, 32, 32, 32, 9, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490616 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490616/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490616 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 221) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/221 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/221' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc4c(cnn4Cc4cccc(F)c4)c3)c2c1) `ZINC001184490616.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490616/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184490616 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc4c(cnn4Cc4cccc(F)c4)c3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 20, 34, 34, 34, 34, 34, 34, 9, 4, 4, 4, 4, 4, 4, 4, 4, 3, 9, 9, 9, 20, 20, 34, 34, 34, 34, 9, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490616 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184490616 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490616/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490616/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490616 Building ZINC001184490616 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490616' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490616 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490616 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490616/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490616 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 220) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/220: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc4c(cnn4Cc4cccc(F)c4)c3)c2c1) `ZINC001184490616.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490616/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184490616 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc4c(cnn4Cc4cccc(F)c4)c3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 20, 32, 32, 32, 32, 32, 32, 9, 4, 4, 4, 4, 4, 4, 4, 4, 3, 9, 9, 9, 20, 20, 32, 32, 32, 32, 9, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490616 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490616/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490616 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 221) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/221: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc4c(cnn4Cc4cccc(F)c4)c3)c2c1) `ZINC001184490616.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490616/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184490616 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc4c(cnn4Cc4cccc(F)c4)c3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 20, 34, 34, 34, 34, 34, 34, 9, 4, 4, 4, 4, 4, 4, 4, 4, 3, 9, 9, 9, 20, 20, 34, 34, 34, 34, 9, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490616 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184490616 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490616/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490616/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490616 Building ZINC001184490751 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490751' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490751 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490751 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490751/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490751 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 222) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/222 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/222' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc4ccn(C(=O)OC(C)(C)C)c4c3)c2c1) `ZINC001184490751.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490751/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184490751 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc4ccn(C(=O)OC(C)(C)C)c4c3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 15, 15, 15, 15, 15, 15, 15, 24, 24, 24, 24, 24, 24, 15, 15, 5, 5, 5, 5, 5, 5, 5, 5, 3, 15, 15, 15, 15, 24, 24, 24, 24, 24, 24, 24, 24, 24, 15, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490751 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490751/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490751 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 223) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/223 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/223' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc4ccn(C(=O)OC(C)(C)C)c4c3)c2c1) `ZINC001184490751.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490751/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184490751 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc4ccn(C(=O)OC(C)(C)C)c4c3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 15, 15, 15, 15, 15, 15, 15, 24, 24, 24, 24, 24, 24, 15, 15, 5, 5, 5, 5, 5, 5, 5, 5, 3, 15, 15, 15, 15, 24, 24, 24, 24, 24, 24, 24, 24, 24, 15, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490751 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184490751 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490751/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490751/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490751 Building ZINC001184490751 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490751' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490751 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490751 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490751/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490751 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 222) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/222: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc4ccn(C(=O)OC(C)(C)C)c4c3)c2c1) `ZINC001184490751.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490751/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184490751 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc4ccn(C(=O)OC(C)(C)C)c4c3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 15, 15, 15, 15, 15, 15, 15, 24, 24, 24, 24, 24, 24, 15, 15, 5, 5, 5, 5, 5, 5, 5, 5, 3, 15, 15, 15, 15, 24, 24, 24, 24, 24, 24, 24, 24, 24, 15, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490751 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490751/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490751 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 223) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/223: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc4ccn(C(=O)OC(C)(C)C)c4c3)c2c1) `ZINC001184490751.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490751/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184490751 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc4ccn(C(=O)OC(C)(C)C)c4c3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 15, 15, 15, 15, 15, 15, 15, 24, 24, 24, 24, 24, 24, 15, 15, 5, 5, 5, 5, 5, 5, 5, 5, 3, 15, 15, 15, 15, 24, 24, 24, 24, 24, 24, 24, 24, 24, 15, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490751 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184490751 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490751/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490751/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490751 Building ZINC001184490788 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184490788 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 224) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/224 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/224' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@@H]4c3ccccc3)c2c1) `ZINC001184490788.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184490788 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@@H]4c3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 3, 3, 3, 14, 22, 22, 22, 15, 22, 22, 22, 22, 22, 22, 22, 23, 23, 22, 23, 23, 8, 8, 8, 8, 8, 8, 8, 8, 3, 19, 22, 22, 22, 22, 22, 22, 22, 22, 22, 23, 23, 22, 23, 23, 8] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 225) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/225 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/225' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@@H]4c3ccccc3)c2c1) `ZINC001184490788.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184490788 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@@H]4c3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 3, 3, 3, 14, 22, 22, 22, 15, 22, 22, 22, 22, 22, 22, 22, 23, 23, 22, 23, 23, 8, 8, 8, 8, 8, 8, 8, 8, 3, 19, 22, 22, 22, 22, 22, 22, 22, 22, 22, 23, 23, 22, 23, 23, 8] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 226) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/226 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/226' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@@H]4c3ccccc3)c2c1) `ZINC001184490788.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184490788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184490788 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@@H]4c3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 3, 3, 3, 15, 25, 25, 25, 16, 25, 25, 25, 25, 25, 25, 25, 27, 27, 25, 27, 27, 8, 8, 9, 9, 9, 8, 8, 8, 3, 20, 25, 25, 25, 25, 25, 25, 25, 25, 25, 27, 27, 25, 27, 27, 8] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 227) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/227 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/227' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@@H]4c3ccccc3)c2c1) `ZINC001184490788.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184490788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184490788 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@@H]4c3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 3, 3, 3, 15, 25, 25, 25, 16, 25, 25, 25, 25, 25, 25, 25, 27, 27, 25, 27, 27, 8, 8, 9, 9, 9, 8, 8, 8, 3, 20, 25, 25, 25, 25, 25, 25, 25, 25, 25, 27, 27, 25, 27, 27, 8] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184490788 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788 Building ZINC001184490788 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184490788 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 224) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/224: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@@H]4c3ccccc3)c2c1) `ZINC001184490788.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184490788 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@@H]4c3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 3, 3, 3, 14, 22, 22, 22, 15, 22, 22, 22, 22, 22, 22, 22, 23, 23, 22, 23, 23, 8, 8, 8, 8, 8, 8, 8, 8, 3, 19, 22, 22, 22, 22, 22, 22, 22, 22, 22, 23, 23, 22, 23, 23, 8] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 225) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/225: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@@H]4c3ccccc3)c2c1) `ZINC001184490788.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184490788 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@@H]4c3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 3, 3, 3, 14, 22, 22, 22, 15, 22, 22, 22, 22, 22, 22, 22, 23, 23, 22, 23, 23, 8, 8, 8, 8, 8, 8, 8, 8, 3, 19, 22, 22, 22, 22, 22, 22, 22, 22, 22, 23, 23, 22, 23, 23, 8] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 226) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/226: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@@H]4c3ccccc3)c2c1) `ZINC001184490788.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184490788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184490788 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@@H]4c3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 3, 3, 3, 15, 25, 25, 25, 16, 25, 25, 25, 25, 25, 25, 25, 27, 27, 25, 27, 27, 8, 8, 9, 9, 9, 8, 8, 8, 3, 20, 25, 25, 25, 25, 25, 25, 25, 25, 25, 27, 27, 25, 27, 27, 8] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 227) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/227: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@@H]4c3ccccc3)c2c1) `ZINC001184490788.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184490788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184490788 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@@H]4c3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 3, 3, 3, 15, 25, 25, 25, 16, 25, 25, 25, 25, 25, 25, 25, 27, 27, 25, 27, 27, 8, 8, 9, 9, 9, 8, 8, 8, 3, 20, 25, 25, 25, 25, 25, 25, 25, 25, 25, 27, 27, 25, 27, 27, 8] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184490788 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788 Building ZINC001184490788 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184490788 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 224) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/224: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@@H]4c3ccccc3)c2c1) `ZINC001184490788.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184490788 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@@H]4c3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 3, 3, 3, 14, 22, 22, 22, 15, 22, 22, 22, 22, 22, 22, 22, 23, 23, 22, 23, 23, 8, 8, 8, 8, 8, 8, 8, 8, 3, 19, 22, 22, 22, 22, 22, 22, 22, 22, 22, 23, 23, 22, 23, 23, 8] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 225) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/225: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@@H]4c3ccccc3)c2c1) `ZINC001184490788.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184490788 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@@H]4c3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 3, 3, 3, 14, 22, 22, 22, 15, 22, 22, 22, 22, 22, 22, 22, 23, 23, 22, 23, 23, 8, 8, 8, 8, 8, 8, 8, 8, 3, 19, 22, 22, 22, 22, 22, 22, 22, 22, 22, 23, 23, 22, 23, 23, 8] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 226) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/226: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@@H]4c3ccccc3)c2c1) `ZINC001184490788.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184490788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184490788 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@@H]4c3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 3, 3, 3, 15, 25, 25, 25, 16, 25, 25, 25, 25, 25, 25, 25, 27, 27, 25, 27, 27, 8, 8, 9, 9, 9, 8, 8, 8, 3, 20, 25, 25, 25, 25, 25, 25, 25, 25, 25, 27, 27, 25, 27, 27, 8] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 227) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/227: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@@H]4c3ccccc3)c2c1) `ZINC001184490788.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184490788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184490788 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@@H]4c3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 3, 3, 3, 15, 25, 25, 25, 16, 25, 25, 25, 25, 25, 25, 25, 27, 27, 25, 27, 27, 8, 8, 9, 9, 9, 8, 8, 8, 3, 20, 25, 25, 25, 25, 25, 25, 25, 25, 25, 27, 27, 25, 27, 27, 8] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184490788 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788 Building ZINC001184490788 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184490788 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 224) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/224: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@@H]4c3ccccc3)c2c1) `ZINC001184490788.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184490788 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@@H]4c3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 3, 3, 3, 14, 22, 22, 22, 15, 22, 22, 22, 22, 22, 22, 22, 23, 23, 22, 23, 23, 8, 8, 8, 8, 8, 8, 8, 8, 3, 19, 22, 22, 22, 22, 22, 22, 22, 22, 22, 23, 23, 22, 23, 23, 8] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 225) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/225: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@@H]4c3ccccc3)c2c1) `ZINC001184490788.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184490788 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@@H]4c3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 3, 3, 3, 14, 22, 22, 22, 15, 22, 22, 22, 22, 22, 22, 22, 23, 23, 22, 23, 23, 8, 8, 8, 8, 8, 8, 8, 8, 3, 19, 22, 22, 22, 22, 22, 22, 22, 22, 22, 23, 23, 22, 23, 23, 8] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 226) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/226: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@@H]4c3ccccc3)c2c1) `ZINC001184490788.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184490788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184490788 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@@H]4c3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 3, 3, 3, 15, 25, 25, 25, 16, 25, 25, 25, 25, 25, 25, 25, 27, 27, 25, 27, 27, 8, 8, 9, 9, 9, 8, 8, 8, 3, 20, 25, 25, 25, 25, 25, 25, 25, 25, 25, 27, 27, 25, 27, 27, 8] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 227) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/227: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@@H]4c3ccccc3)c2c1) `ZINC001184490788.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184490788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184490788 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@@H]4c3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 3, 3, 3, 15, 25, 25, 25, 16, 25, 25, 25, 25, 25, 25, 25, 27, 27, 25, 27, 27, 8, 8, 9, 9, 9, 8, 8, 8, 3, 20, 25, 25, 25, 25, 25, 25, 25, 25, 25, 27, 27, 25, 27, 27, 8] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184490788 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490788 Building ZINC001184490789 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184490789 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 228) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/228 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/228' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@H]4c3ccccc3)c2c1) `ZINC001184490789.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184490789 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@H]4c3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 3, 3, 3, 15, 24, 25, 25, 13, 25, 25, 25, 25, 25, 25, 25, 27, 27, 25, 27, 27, 8, 8, 9, 9, 9, 8, 8, 8, 3, 20, 25, 25, 25, 25, 25, 25, 25, 25, 25, 27, 27, 25, 27, 27, 8] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 229) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/229 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/229' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@H]4c3ccccc3)c2c1) `ZINC001184490789.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184490789 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@H]4c3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 3, 3, 3, 15, 24, 25, 25, 13, 25, 25, 25, 25, 25, 25, 25, 27, 27, 25, 27, 27, 8, 8, 9, 9, 9, 8, 8, 8, 3, 20, 25, 25, 25, 25, 25, 25, 25, 25, 25, 27, 27, 25, 27, 27, 8] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 230) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/230 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/230' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@H]4c3ccccc3)c2c1) `ZINC001184490789.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184490789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184490789 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@H]4c3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 3, 3, 3, 13, 21, 24, 24, 14, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 9, 9, 11, 11, 11, 9, 9, 9, 3, 19, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 9] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 231) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/231 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/231' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@H]4c3ccccc3)c2c1) `ZINC001184490789.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184490789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184490789 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@H]4c3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 3, 3, 3, 13, 21, 24, 24, 14, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 9, 9, 11, 11, 11, 9, 9, 9, 3, 19, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 9] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184490789 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789 Building ZINC001184490789 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184490789 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 228) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/228: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@H]4c3ccccc3)c2c1) `ZINC001184490789.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184490789 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@H]4c3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 3, 3, 3, 15, 24, 25, 25, 13, 25, 25, 25, 25, 25, 25, 25, 27, 27, 25, 27, 27, 8, 8, 9, 9, 9, 8, 8, 8, 3, 20, 25, 25, 25, 25, 25, 25, 25, 25, 25, 27, 27, 25, 27, 27, 8] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 229) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/229: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@H]4c3ccccc3)c2c1) `ZINC001184490789.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184490789 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@H]4c3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 3, 3, 3, 15, 24, 25, 25, 13, 25, 25, 25, 25, 25, 25, 25, 27, 27, 25, 27, 27, 8, 8, 9, 9, 9, 8, 8, 8, 3, 20, 25, 25, 25, 25, 25, 25, 25, 25, 25, 27, 27, 25, 27, 27, 8] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 230) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/230: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@H]4c3ccccc3)c2c1) `ZINC001184490789.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184490789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184490789 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@H]4c3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 3, 3, 3, 13, 21, 24, 24, 14, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 9, 9, 11, 11, 11, 9, 9, 9, 3, 19, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 9] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 231) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/231: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@H]4c3ccccc3)c2c1) `ZINC001184490789.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184490789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184490789 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@H]4c3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 3, 3, 3, 13, 21, 24, 24, 14, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 9, 9, 11, 11, 11, 9, 9, 9, 3, 19, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 9] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184490789 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789 Building ZINC001184490789 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184490789 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 228) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/228: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@H]4c3ccccc3)c2c1) `ZINC001184490789.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184490789 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@H]4c3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 3, 3, 3, 15, 24, 25, 25, 13, 25, 25, 25, 25, 25, 25, 25, 27, 27, 25, 27, 27, 8, 8, 9, 9, 9, 8, 8, 8, 3, 20, 25, 25, 25, 25, 25, 25, 25, 25, 25, 27, 27, 25, 27, 27, 8] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 229) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/229: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@H]4c3ccccc3)c2c1) `ZINC001184490789.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184490789 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@H]4c3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 3, 3, 3, 15, 24, 25, 25, 13, 25, 25, 25, 25, 25, 25, 25, 27, 27, 25, 27, 27, 8, 8, 9, 9, 9, 8, 8, 8, 3, 20, 25, 25, 25, 25, 25, 25, 25, 25, 25, 27, 27, 25, 27, 27, 8] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 230) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/230: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@H]4c3ccccc3)c2c1) `ZINC001184490789.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184490789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184490789 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@H]4c3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 3, 3, 3, 13, 21, 24, 24, 14, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 9, 9, 11, 11, 11, 9, 9, 9, 3, 19, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 9] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 231) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/231: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@H]4c3ccccc3)c2c1) `ZINC001184490789.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184490789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184490789 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@H]4c3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 3, 3, 3, 13, 21, 24, 24, 14, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 9, 9, 11, 11, 11, 9, 9, 9, 3, 19, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 9] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184490789 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789 Building ZINC001184490789 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184490789 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 228) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/228: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@H]4c3ccccc3)c2c1) `ZINC001184490789.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184490789 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@H]4c3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 3, 3, 3, 15, 24, 25, 25, 13, 25, 25, 25, 25, 25, 25, 25, 27, 27, 25, 27, 27, 8, 8, 9, 9, 9, 8, 8, 8, 3, 20, 25, 25, 25, 25, 25, 25, 25, 25, 25, 27, 27, 25, 27, 27, 8] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 229) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/229: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@H]4c3ccccc3)c2c1) `ZINC001184490789.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184490789 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@H]4c3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 3, 3, 3, 15, 24, 25, 25, 13, 25, 25, 25, 25, 25, 25, 25, 27, 27, 25, 27, 27, 8, 8, 9, 9, 9, 8, 8, 8, 3, 20, 25, 25, 25, 25, 25, 25, 25, 25, 25, 27, 27, 25, 27, 27, 8] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 230) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/230: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@H]4c3ccccc3)c2c1) `ZINC001184490789.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184490789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184490789 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@H]4c3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 3, 3, 3, 13, 21, 24, 24, 14, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 9, 9, 11, 11, 11, 9, 9, 9, 3, 19, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 9] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 231) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/231: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@H]4c3ccccc3)c2c1) `ZINC001184490789.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184490789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184490789 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3CN(C)C[C@H]4c3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 3, 3, 3, 13, 21, 24, 24, 14, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 9, 9, 11, 11, 11, 9, 9, 9, 3, 19, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 9] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184490789 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490789 Building ZINC001184490813 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490813' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490813 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490813 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490813/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490813 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 232) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/232 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/232' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOP(=O)(Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)cc1)OCC) `ZINC001184490813.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184490813 none CCOP(=O)(Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)cc1)OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'P.3', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 13, 11, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 16, 19, 10, 10, 10, 10, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 19, 28, 30, 31, 31, 31, 31, 31, 16, 16, 10, 10, 3, 4, 4, 4, 4, 4, 4, 4, 10, 10, 30, 30, 30, 30, 30] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490813 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490813/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490813 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 233) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/233 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/233' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOP(=O)(Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)cc1)OCC) `ZINC001184490813.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490813/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184490813 none CCOP(=O)(Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)cc1)OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'P.3', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 13, 11, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 20, 16, 20, 3, 3, 10, 10, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 20, 31, 31, 31, 31, 31, 31, 31, 16, 16, 10, 10, 3, 4, 4, 4, 4, 4, 4, 4, 10, 10, 31, 31, 31, 31, 31] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490813 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184490813 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490813/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490813/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490813 Building ZINC001184490813 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490813' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490813 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490813 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490813/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490813 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 232) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/232: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOP(=O)(Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)cc1)OCC) `ZINC001184490813.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184490813 none CCOP(=O)(Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)cc1)OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'P.3', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 13, 11, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 16, 19, 10, 10, 10, 10, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 19, 28, 30, 31, 31, 31, 31, 31, 16, 16, 10, 10, 3, 4, 4, 4, 4, 4, 4, 4, 10, 10, 30, 30, 30, 30, 30] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490813 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490813/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490813 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 233) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/233: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOP(=O)(Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)cc1)OCC) `ZINC001184490813.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490813/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184490813 none CCOP(=O)(Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)cc1)OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'P.3', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 13, 11, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 20, 16, 20, 3, 3, 10, 10, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 20, 31, 31, 31, 31, 31, 31, 31, 16, 16, 10, 10, 3, 4, 4, 4, 4, 4, 4, 4, 10, 10, 31, 31, 31, 31, 31] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490813 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184490813 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490813/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490813/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490813 Building ZINC001184490856 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490856' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490856 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490856 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490856/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490856 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 234) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/234 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/234' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC(Cc4c(F)cccc4Cl)CC3)c2c1) `ZINC001184490856.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184490856 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC(Cc4c(F)cccc4Cl)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 15, 1, 1, 1, 1, 16, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 2, 4, 5, 5, 5, 5, 13, 23, 23, 23, 23, 23, 23, 23, 5, 5, 4, 4, 5, 5, 5, 4, 4, 4, 5, 5, 5, 5, 5, 13, 13, 23, 23, 23, 5, 5, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490856 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490856/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490856 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 235) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/235 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/235' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC(Cc4c(F)cccc4Cl)CC3)c2c1) `ZINC001184490856.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490856/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184490856 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC(Cc4c(F)cccc4Cl)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 15, 1, 1, 1, 1, 16, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 12, 26, 26, 26, 22, 26, 26, 26, 4, 4, 5, 5, 6, 6, 6, 5, 5, 5, 4, 4, 4, 4, 4, 12, 12, 26, 25, 26, 4, 4, 4, 4, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490856 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184490856 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490856/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490856/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490856 Building ZINC001184490856 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490856' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490856 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490856 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490856/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490856 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 234) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/234: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC(Cc4c(F)cccc4Cl)CC3)c2c1) `ZINC001184490856.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184490856 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC(Cc4c(F)cccc4Cl)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 15, 1, 1, 1, 1, 16, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 2, 4, 5, 5, 5, 5, 13, 23, 23, 23, 23, 23, 23, 23, 5, 5, 4, 4, 5, 5, 5, 4, 4, 4, 5, 5, 5, 5, 5, 13, 13, 23, 23, 23, 5, 5, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490856 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490856/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490856 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 235) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/235: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC(Cc4c(F)cccc4Cl)CC3)c2c1) `ZINC001184490856.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490856/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184490856 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC(Cc4c(F)cccc4Cl)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 15, 1, 1, 1, 1, 16, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 12, 26, 26, 26, 22, 26, 26, 26, 4, 4, 5, 5, 6, 6, 6, 5, 5, 5, 4, 4, 4, 4, 4, 12, 12, 26, 25, 26, 4, 4, 4, 4, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490856 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184490856 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490856/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490856/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184490856 Building ZINC001184491081 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491081' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491081 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184491081 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491081/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491081 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 236) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/236 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/236' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(OCc4ccccn4)c(Cl)c3)c2c1) `ZINC001184491081.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491081/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184491081 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(OCc4ccccn4)c(Cl)c3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 8, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 26, 35, 42, 42, 42, 42, 42, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 3, 10, 10, 35, 35, 42, 42, 42, 42, 10, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491081 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491081/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491081 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 237) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/237 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/237' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(OCc4ccccn4)c(Cl)c3)c2c1) `ZINC001184491081.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491081/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184491081 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(OCc4ccccn4)c(Cl)c3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 8, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 25, 34, 41, 41, 41, 41, 41, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 3, 10, 10, 34, 34, 41, 41, 41, 41, 10, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491081 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184491081 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491081/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491081/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491081 Building ZINC001184491081 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491081' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491081 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184491081 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491081/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491081 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 236) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/236: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(OCc4ccccn4)c(Cl)c3)c2c1) `ZINC001184491081.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491081/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184491081 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(OCc4ccccn4)c(Cl)c3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 8, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 26, 35, 42, 42, 42, 42, 42, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 3, 10, 10, 35, 35, 42, 42, 42, 42, 10, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491081 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491081/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491081 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 237) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/237: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(OCc4ccccn4)c(Cl)c3)c2c1) `ZINC001184491081.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491081/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184491081 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(OCc4ccccn4)c(Cl)c3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 8, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 25, 34, 41, 41, 41, 41, 41, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 3, 10, 10, 34, 34, 41, 41, 41, 41, 10, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491081 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184491081 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491081/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491081/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491081 Building ZINC001184491096 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491096' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491096 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184491096 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491096/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491096 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 238) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/238 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/238' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(CCc4ccc(N)cc4C)c(C)c3)c2c1) `ZINC001184491096.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184491096 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(CCc4ccc(N)cc4C)c(C)c3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 5, 1, 1, 1, 1, 8, 1, 1, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 10, 10, 3, 10, 20, 20, 34, 34, 20, 34, 34, 34, 32, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 3, 10, 10, 20, 20, 20, 20, 34, 34, 34, 34, 34, 34, 34, 34, 10, 10, 10, 10, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491096 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491096/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491096 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 239) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/239 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/239' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(CCc4ccc(N)cc4C)c(C)c3)c2c1) `ZINC001184491096.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491096/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184491096 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(CCc4ccc(N)cc4C)c(C)c3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 5, 1, 1, 1, 1, 8, 1, 1, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 10, 10, 3, 3, 10, 10, 20, 31, 11, 17, 32, 20, 20, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 3, 10, 10, 10, 10, 10, 10, 20, 34, 34, 34, 34, 20, 20, 20, 10, 10, 10, 10, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491096 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184491096 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491096/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491096/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491096 Building ZINC001184491096 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491096' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491096 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184491096 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491096/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491096 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 238) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/238: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(CCc4ccc(N)cc4C)c(C)c3)c2c1) `ZINC001184491096.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184491096 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(CCc4ccc(N)cc4C)c(C)c3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 5, 1, 1, 1, 1, 8, 1, 1, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 10, 10, 3, 10, 20, 20, 34, 34, 20, 34, 34, 34, 32, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 3, 10, 10, 20, 20, 20, 20, 34, 34, 34, 34, 34, 34, 34, 34, 10, 10, 10, 10, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491096 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491096/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491096 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 239) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/239: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(CCc4ccc(N)cc4C)c(C)c3)c2c1) `ZINC001184491096.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491096/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001184491096 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(CCc4ccc(N)cc4C)c(C)c3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 5, 1, 1, 1, 1, 8, 1, 1, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 10, 10, 3, 3, 10, 10, 20, 31, 11, 17, 32, 20, 20, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 3, 10, 10, 10, 10, 10, 10, 20, 34, 34, 34, 34, 20, 20, 20, 10, 10, 10, 10, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491096 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184491096 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491096/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491096/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491096 Building ZINC001184491368 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491368' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491368 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184491368 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491368/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491368 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 240) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/240 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/240' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc4oc(c5ccc(N)cc5)cc4c3)c2c1) `ZINC001184491368.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491368/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491368 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc4oc(c5ccc(N)cc5)cc4c3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 15, 15, 15, 15, 15, 15, 33, 33, 15, 24, 33, 33, 15, 15, 15, 7, 7, 8, 8, 8, 7, 7, 7, 3, 15, 15, 33, 33, 33, 33, 33, 33, 15, 15, 7] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491368 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491368/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491368 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 241) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/241 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/241' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc4oc(c5ccc(N)cc5)cc4c3)c2c1) `ZINC001184491368.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491368/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491368 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc4oc(c5ccc(N)cc5)cc4c3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 15, 15, 15, 15, 15, 15, 30, 30, 15, 21, 30, 30, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 3, 15, 15, 30, 30, 30, 30, 30, 30, 15, 15, 7] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491368 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184491368 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491368/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491368/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491368 Building ZINC001184491368 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491368' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491368 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184491368 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491368/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491368 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 240) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/240: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc4oc(c5ccc(N)cc5)cc4c3)c2c1) `ZINC001184491368.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491368/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491368 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc4oc(c5ccc(N)cc5)cc4c3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 15, 15, 15, 15, 15, 15, 33, 33, 15, 24, 33, 33, 15, 15, 15, 7, 7, 8, 8, 8, 7, 7, 7, 3, 15, 15, 33, 33, 33, 33, 33, 33, 15, 15, 7] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491368 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491368/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491368 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 241) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/241: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc4oc(c5ccc(N)cc5)cc4c3)c2c1) `ZINC001184491368.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491368/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491368 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc4oc(c5ccc(N)cc5)cc4c3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 15, 15, 15, 15, 15, 15, 30, 30, 15, 21, 30, 30, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 3, 15, 15, 30, 30, 30, 30, 30, 30, 15, 15, 7] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491368 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184491368 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491368/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491368/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491368 Building ZINC001184491414 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491414' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491414 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184491414 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491414/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491414 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 242) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/242 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/242' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccccc3C(=O)Nc3ccccc3C)c2c1) `ZINC001184491414.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491414/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491414 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccccc3C(=O)Nc3ccccc3C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 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: [8, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 12, 12, 12, 18, 16, 16, 24, 24, 18, 24, 24, 24, 7, 7, 8, 8, 8, 7, 7, 7, 5, 12, 12, 12, 12, 18, 23, 24, 18, 24, 24, 24, 24, 7] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 86 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491414 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491414/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491414 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 243) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/243 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/243' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccccc3C(=O)Nc3ccccc3C)c2c1) `ZINC001184491414.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491414/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491414 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccccc3C(=O)Nc3ccccc3C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 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: [8, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 5, 5, 5, 11, 11, 11, 11, 11, 11, 18, 18, 18, 24, 24, 21, 24, 24, 23, 7, 7, 8, 8, 8, 7, 7, 7, 5, 11, 11, 11, 11, 18, 24, 24, 21, 24, 23, 23, 23, 7] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 74 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491414 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184491414 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491414/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491414/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491414 Building ZINC001184491414 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491414' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491414 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184491414 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491414/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491414 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 242) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/242: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccccc3C(=O)Nc3ccccc3C)c2c1) `ZINC001184491414.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491414/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491414 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccccc3C(=O)Nc3ccccc3C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 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: [8, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 12, 12, 12, 18, 16, 16, 24, 24, 18, 24, 24, 24, 7, 7, 8, 8, 8, 7, 7, 7, 5, 12, 12, 12, 12, 18, 23, 24, 18, 24, 24, 24, 24, 7] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 86 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491414 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491414/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491414 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 243) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/243: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccccc3C(=O)Nc3ccccc3C)c2c1) `ZINC001184491414.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491414/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491414 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccccc3C(=O)Nc3ccccc3C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 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: [8, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 5, 5, 5, 11, 11, 11, 11, 11, 11, 18, 18, 18, 24, 24, 21, 24, 24, 23, 7, 7, 8, 8, 8, 7, 7, 7, 5, 11, 11, 11, 11, 18, 24, 24, 21, 24, 23, 23, 23, 7] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 74 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491414 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184491414 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491414/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491414/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184491414 Building ZINC001184493843 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184493843' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184493843 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184493843 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184493843/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184493843 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 244) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/244 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/244' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NC3(c4ccc(F)cc4)CCC(F)(F)CC3)c2c1) `ZINC001184493843.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184493843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184493843/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184493843 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NC3(c4ccc(F)cc4)CCC(F)(F)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'F', 'F', '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, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 15, 15, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 5, 5, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 6, 6, 6, 6, 6, 6, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 49 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184493843 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184493843/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184493843 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 245) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/245 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/245' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NC3(c4ccc(F)cc4)CCC(F)(F)CC3)c2c1) `ZINC001184493843.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184493843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184493843/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184493843 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NC3(c4ccc(F)cc4)CCC(F)(F)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'F', 'F', '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, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 15, 15, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 5, 5, 6, 15, 19, 19, 16, 18, 19, 19, 15, 15, 15, 15, 15, 15, 15, 7, 7, 8, 8, 8, 7, 7, 7, 5, 19, 19, 19, 19, 15, 15, 15, 15, 15, 15, 15, 15, 7] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 68 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184493843 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184493843 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184493843/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184493843/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184493843 Building ZINC001184493843 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184493843' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184493843 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184493843 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184493843/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184493843 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 244) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/244: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NC3(c4ccc(F)cc4)CCC(F)(F)CC3)c2c1) `ZINC001184493843.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184493843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184493843/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184493843 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NC3(c4ccc(F)cc4)CCC(F)(F)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'F', 'F', '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, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 15, 15, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 5, 5, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 6, 6, 6, 6, 6, 6, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 49 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184493843 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184493843/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184493843 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 245) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/245: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NC3(c4ccc(F)cc4)CCC(F)(F)CC3)c2c1) `ZINC001184493843.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184493843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184493843/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184493843 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NC3(c4ccc(F)cc4)CCC(F)(F)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'F', 'F', '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, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 15, 15, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 5, 5, 6, 15, 19, 19, 16, 18, 19, 19, 15, 15, 15, 15, 15, 15, 15, 7, 7, 8, 8, 8, 7, 7, 7, 5, 19, 19, 19, 19, 15, 15, 15, 15, 15, 15, 15, 15, 7] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 68 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184493843 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184493843 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184493843/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184493843/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184493843 Building ZINC001184494067 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184494067' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184494067 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184494067 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184494067/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184494067 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 246) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/246 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/246' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NC3(c4ccccc4OC)CCC(F)(F)CC3)c2c1) `ZINC001184494067.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184494067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184494067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184494067 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NC3(c4ccccc4OC)CCC(F)(F)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 15, 15, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 5, 5, 5, 16, 19, 19, 19, 19, 19, 19, 19, 16, 16, 16, 16, 16, 16, 16, 6, 6, 6, 6, 6, 6, 6, 6, 5, 19, 19, 19, 19, 19, 19, 19, 16, 16, 16, 16, 16, 16, 16, 16, 6] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 53 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184494067 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184494067/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184494067 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 247) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/247 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/247' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NC3(c4ccccc4OC)CCC(F)(F)CC3)c2c1) `ZINC001184494067.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184494067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184494067/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184494067 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NC3(c4ccccc4OC)CCC(F)(F)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 15, 15, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 4, 14, 20, 20, 20, 20, 20, 20, 20, 14, 14, 14, 14, 14, 14, 14, 5, 5, 6, 6, 6, 5, 5, 5, 4, 20, 20, 20, 20, 20, 20, 20, 14, 14, 14, 14, 14, 14, 14, 14, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 53 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184494067 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184494067 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184494067/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184494067/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184494067 Building ZINC001184494067 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184494067' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184494067 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184494067 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184494067/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184494067 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 246) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/246: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NC3(c4ccccc4OC)CCC(F)(F)CC3)c2c1) `ZINC001184494067.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184494067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184494067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184494067 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NC3(c4ccccc4OC)CCC(F)(F)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 15, 15, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 5, 5, 5, 16, 19, 19, 19, 19, 19, 19, 19, 16, 16, 16, 16, 16, 16, 16, 6, 6, 6, 6, 6, 6, 6, 6, 5, 19, 19, 19, 19, 19, 19, 19, 16, 16, 16, 16, 16, 16, 16, 16, 6] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 53 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184494067 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184494067/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184494067 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 247) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/247: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NC3(c4ccccc4OC)CCC(F)(F)CC3)c2c1) `ZINC001184494067.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184494067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184494067/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184494067 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NC3(c4ccccc4OC)CCC(F)(F)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 15, 15, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 4, 14, 20, 20, 20, 20, 20, 20, 20, 14, 14, 14, 14, 14, 14, 14, 5, 5, 6, 6, 6, 5, 5, 5, 4, 20, 20, 20, 20, 20, 20, 20, 14, 14, 14, 14, 14, 14, 14, 14, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 53 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184494067 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184494067 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184494067/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184494067/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184494067 Building ZINC001184495252 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184495252' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184495252 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184495252 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184495252/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184495252 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 248) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/248 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/248' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NC3(Cc4ccccc4)CCC(F)(F)CC3)c2c1) `ZINC001184495252.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184495252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184495252/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184495252 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NC3(Cc4ccccc4)CCC(F)(F)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 4, 7, 20, 20, 20, 20, 20, 20, 7, 7, 7, 7, 7, 7, 7, 5, 5, 7, 7, 7, 5, 5, 5, 4, 20, 20, 20, 20, 20, 20, 20, 7, 7, 7, 7, 7, 7, 7, 7, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184495252 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184495252/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184495252 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 249) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/249 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/249' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NC3(Cc4ccccc4)CCC(F)(F)CC3)c2c1) `ZINC001184495252.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184495252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184495252/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184495252 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NC3(Cc4ccccc4)CCC(F)(F)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 4, 7, 21, 21, 21, 21, 21, 21, 7, 7, 7, 7, 7, 7, 7, 5, 5, 6, 6, 6, 5, 5, 5, 4, 21, 21, 21, 21, 21, 21, 21, 7, 7, 7, 7, 7, 7, 7, 7, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184495252 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184495252 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184495252/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184495252/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184495252 Building ZINC001184495252 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184495252' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184495252 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184495252 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184495252/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184495252 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 248) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/248: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NC3(Cc4ccccc4)CCC(F)(F)CC3)c2c1) `ZINC001184495252.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184495252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184495252/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184495252 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NC3(Cc4ccccc4)CCC(F)(F)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 4, 7, 20, 20, 20, 20, 20, 20, 7, 7, 7, 7, 7, 7, 7, 5, 5, 7, 7, 7, 5, 5, 5, 4, 20, 20, 20, 20, 20, 20, 20, 7, 7, 7, 7, 7, 7, 7, 7, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184495252 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184495252/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184495252 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 249) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/249: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NC3(Cc4ccccc4)CCC(F)(F)CC3)c2c1) `ZINC001184495252.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184495252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184495252/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184495252 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NC3(Cc4ccccc4)CCC(F)(F)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 4, 7, 21, 21, 21, 21, 21, 21, 7, 7, 7, 7, 7, 7, 7, 5, 5, 6, 6, 6, 5, 5, 5, 4, 21, 21, 21, 21, 21, 21, 21, 7, 7, 7, 7, 7, 7, 7, 7, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184495252 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184495252 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184495252/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184495252/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184495252 Building ZINC001184477934 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184477934' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184477934 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184477934 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184477934/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184477934 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 250) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/250 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/250' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnn(c2ccc(C)cc2)c1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184477934.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184477934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184477934/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001184477934 none Cc1cnn(c2ccc(C)cc2)c1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 20, 20, 20, 10, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184477934 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184477934/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184477934 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 251) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/251 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/251' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnn(c2ccc(C)cc2)c1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184477934.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184477934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184477934/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001184477934 none Cc1cnn(c2ccc(C)cc2)c1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 20, 20, 20, 10, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184477934 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184477934 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184477934/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184477934/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184477934 Building ZINC001184477934 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184477934' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184477934 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184477934 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184477934/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184477934 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 250) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/250: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnn(c2ccc(C)cc2)c1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184477934.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184477934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184477934/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001184477934 none Cc1cnn(c2ccc(C)cc2)c1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 20, 20, 20, 10, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184477934 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184477934/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184477934 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 251) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/251: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnn(c2ccc(C)cc2)c1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184477934.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184477934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184477934/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001184477934 none Cc1cnn(c2ccc(C)cc2)c1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 20, 20, 20, 10, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184477934 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184477934 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184477934/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184477934/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184477934 Building ZINC001184478316 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478316' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478316 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184478316 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478316/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478316 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 252) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/252 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/252' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc2c(F)cccc2cc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478316.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478316/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001184478316 none Cc1nc2c(F)cccc2cc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 15, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 26, 26, 26, 26, 26, 26, 26, 6, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478316 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478316/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478316 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 253) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/253 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/253' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc2c(F)cccc2cc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478316.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478316/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001184478316 none Cc1nc2c(F)cccc2cc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 15, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 26, 26, 26, 26, 26, 26, 26, 6, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478316 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184478316 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478316/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478316/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478316 Building ZINC001184478316 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478316' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478316 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184478316 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478316/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478316 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 252) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/252: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc2c(F)cccc2cc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478316.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478316/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001184478316 none Cc1nc2c(F)cccc2cc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 15, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 26, 26, 26, 26, 26, 26, 26, 6, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478316 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478316/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478316 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 253) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/253: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc2c(F)cccc2cc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478316.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478316/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001184478316 none Cc1nc2c(F)cccc2cc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 15, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 26, 26, 26, 26, 26, 26, 26, 6, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478316 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184478316 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478316/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478316/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478316 Building ZINC001184478494 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478494' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478494 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184478494 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478494/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478494 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 254) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/254 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/254' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(CCc2ccccn2)c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478494.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001184478494 none O=C(Nc1cccc(CCc2ccccn2)c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 5, 1, 1, 1, 1, 1, 8, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 11, 11, 11, 11, 11, 22, 22, 29, 29, 29, 29, 29, 11, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 11, 11, 11, 22, 22, 22, 22, 29, 29, 29, 29, 11, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478494 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478494/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478494 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 255) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/255 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/255' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(CCc2ccccn2)c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478494.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478494/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001184478494 none O=C(Nc1cccc(CCc2ccccn2)c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 5, 1, 1, 1, 1, 1, 8, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 11, 11, 11, 11, 11, 22, 22, 29, 29, 29, 29, 29, 11, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 11, 11, 11, 22, 22, 22, 22, 29, 29, 29, 29, 11, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478494 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184478494 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478494/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478494/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478494 Building ZINC001184478494 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478494' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478494 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184478494 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478494/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478494 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 254) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/254: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(CCc2ccccn2)c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478494.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001184478494 none O=C(Nc1cccc(CCc2ccccn2)c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 5, 1, 1, 1, 1, 1, 8, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 11, 11, 11, 11, 11, 22, 22, 29, 29, 29, 29, 29, 11, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 11, 11, 11, 22, 22, 22, 22, 29, 29, 29, 29, 11, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478494 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478494/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478494 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 255) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/255: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(CCc2ccccn2)c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478494.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478494/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001184478494 none O=C(Nc1cccc(CCc2ccccn2)c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 5, 1, 1, 1, 1, 1, 8, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 11, 11, 11, 11, 11, 22, 22, 29, 29, 29, 29, 29, 11, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 11, 11, 11, 22, 22, 22, 22, 29, 29, 29, 29, 11, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478494 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184478494 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478494/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478494/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478494 Building ZINC001184478829 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478829' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478829 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184478829 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478829/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478829 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 256) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/256 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/256' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cnc2cc(Cl)ccc2c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478829.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478829/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001184478829 none O=C(Nc1cnc2cc(Cl)ccc2c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 8, 1, 1, 1, 16, 1, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 22, 22, 22, 22, 22, 9, 9, 9, 9] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478829 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478829/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478829 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 257) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/257 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/257' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cnc2cc(Cl)ccc2c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478829.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478829/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001184478829 none O=C(Nc1cnc2cc(Cl)ccc2c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 8, 1, 1, 1, 16, 1, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 22, 22, 22, 22, 22, 9, 9, 9, 9] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478829 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184478829 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478829/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478829/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478829 Building ZINC001184478829 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478829' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478829 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184478829 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478829/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478829 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 256) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/256: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cnc2cc(Cl)ccc2c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478829.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478829/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001184478829 none O=C(Nc1cnc2cc(Cl)ccc2c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 8, 1, 1, 1, 16, 1, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 22, 22, 22, 22, 22, 9, 9, 9, 9] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478829 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478829/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478829 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 257) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/257: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cnc2cc(Cl)ccc2c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478829.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478829/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001184478829 none O=C(Nc1cnc2cc(Cl)ccc2c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 8, 1, 1, 1, 16, 1, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 22, 22, 22, 22, 22, 9, 9, 9, 9] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478829 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184478829 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478829/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478829/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184478829 Building ZINC001184479766 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479766' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479766 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479766 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479766/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479766 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 258) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/258 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/258' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCn2cccc2[C@@H]1c1ccccc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479766.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479766/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184479766 none O=C(N1CCn2cccc2[C@@H]1c1ccccc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 9, 9, 9, 9] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 36 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479766 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479766/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479766 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 259) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/259 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/259' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCn2cccc2[C@@H]1c1ccccc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479766.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479766/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184479766 none O=C(N1CCn2cccc2[C@@H]1c1ccccc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 16, 16, 14, 16, 16, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 14, 14, 14, 14, 14, 14, 14, 16, 16, 16, 16, 16, 9, 9, 9, 9] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479766 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184479766 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479766/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479766/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479766 Building ZINC001184479766 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479766' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479766 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479766 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479766/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479766 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 258) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/258: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCn2cccc2[C@@H]1c1ccccc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479766.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479766/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184479766 none O=C(N1CCn2cccc2[C@@H]1c1ccccc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 9, 9, 9, 9] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 36 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479766 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479766/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479766 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 259) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/259: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCn2cccc2[C@@H]1c1ccccc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479766.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479766/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184479766 none O=C(N1CCn2cccc2[C@@H]1c1ccccc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 16, 16, 14, 16, 16, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 14, 14, 14, 14, 14, 14, 14, 16, 16, 16, 16, 16, 9, 9, 9, 9] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479766 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184479766 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479766/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479766/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479766 Building ZINC001184479767 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479767' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479767 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479767 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479767/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479767 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 260) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/260 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/260' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCn2cccc2[C@H]1c1ccccc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479767.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479767/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184479767 none O=C(N1CCn2cccc2[C@H]1c1ccccc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 17, 17, 17, 17, 17, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 14, 14, 14, 14, 14, 14, 14, 17, 17, 14, 17, 17, 9, 9, 9, 9] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479767 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479767/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479767 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 261) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/261 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/261' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCn2cccc2[C@H]1c1ccccc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479767.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479767/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184479767 none O=C(N1CCn2cccc2[C@H]1c1ccccc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 9, 9, 9, 9] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 36 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479767 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184479767 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479767/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479767/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479767 Building ZINC001184479767 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479767' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479767 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479767 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479767/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479767 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 260) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/260: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCn2cccc2[C@H]1c1ccccc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479767.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479767/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184479767 none O=C(N1CCn2cccc2[C@H]1c1ccccc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 17, 17, 17, 17, 17, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 14, 14, 14, 14, 14, 14, 14, 17, 17, 14, 17, 17, 9, 9, 9, 9] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479767 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479767/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479767 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 261) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/261: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCn2cccc2[C@H]1c1ccccc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479767.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479767/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184479767 none O=C(N1CCn2cccc2[C@H]1c1ccccc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 9, 9, 9, 9] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 36 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479767 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184479767 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479767/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479767/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479767 Building ZINC001184479364 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479364' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479364 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479364 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479364/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479364 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 262) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/262 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/262' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc(Cl)c(Cl)nc1Cl)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479364.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001184479364 none O=C(Nc1nc(Cl)c(Cl)nc1Cl)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 16, 1, 16, 8, 1, 16, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 3, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 9, 9, 9, 9] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479364 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479364/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479364 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 263) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/263 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/263' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc(Cl)c(Cl)nc1Cl)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479364.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479364/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001184479364 none O=C(Nc1nc(Cl)c(Cl)nc1Cl)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 16, 1, 16, 8, 1, 16, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 3, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 9, 9, 9, 9] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479364 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184479364 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479364/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479364/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479364 Building ZINC001184479364 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479364' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479364 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479364 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479364/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479364 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 262) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/262: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc(Cl)c(Cl)nc1Cl)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479364.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001184479364 none O=C(Nc1nc(Cl)c(Cl)nc1Cl)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 16, 1, 16, 8, 1, 16, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 3, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 9, 9, 9, 9] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479364 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479364/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479364 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 263) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/263: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc(Cl)c(Cl)nc1Cl)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479364.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479364/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001184479364 none O=C(Nc1nc(Cl)c(Cl)nc1Cl)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 16, 1, 16, 8, 1, 16, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 3, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 9, 9, 9, 9] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479364 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184479364 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479364/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479364/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479364 Building ZINC001184479578 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479578' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479578 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479578 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479578/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479578 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 264) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/264 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/264' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(F)c(Cl)nc1Cl)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479578.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479578/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001184479578 none O=C(Nc1cc(F)c(Cl)nc1Cl)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 15, 1, 16, 8, 1, 16, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 26, 9, 9, 9, 9] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479578 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479578/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479578 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 265) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/265 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/265' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(F)c(Cl)nc1Cl)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479578.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479578/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001184479578 none O=C(Nc1cc(F)c(Cl)nc1Cl)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 15, 1, 16, 8, 1, 16, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 26, 9, 9, 9, 9] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479578 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184479578 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479578/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479578/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479578 Building ZINC001184479578 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479578' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479578 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479578 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479578/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479578 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 264) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/264: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(F)c(Cl)nc1Cl)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479578.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479578/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001184479578 none O=C(Nc1cc(F)c(Cl)nc1Cl)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 15, 1, 16, 8, 1, 16, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 26, 9, 9, 9, 9] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479578 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479578/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479578 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 265) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/265: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(F)c(Cl)nc1Cl)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479578.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479578/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001184479578 none O=C(Nc1cc(F)c(Cl)nc1Cl)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 15, 1, 16, 8, 1, 16, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 26, 9, 9, 9, 9] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479578 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184479578 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479578/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479578/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184479578 Building ZINC001184480205 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480205' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480205 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480205 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480205/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480205 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 266) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/266 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/266' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ncc(c2ccccc2)s1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480205.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480205/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001184480205 none O=C(Nc1ncc(c2ccccc2)s1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 10, 10, 10, 10, 28, 28, 16, 28, 28, 10, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 10, 28, 28, 20, 28, 28, 9, 9, 9, 9] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480205 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480205/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480205 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 267) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/267 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/267' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ncc(c2ccccc2)s1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480205.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480205/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001184480205 none O=C(Nc1ncc(c2ccccc2)s1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 10, 10, 10, 10, 28, 28, 10, 28, 28, 10, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 10, 28, 28, 10, 28, 28, 9, 9, 9, 9] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480205 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184480205 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480205/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480205/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480205 Building ZINC001184480205 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480205' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480205 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480205 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480205/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480205 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 266) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/266: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ncc(c2ccccc2)s1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480205.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480205/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001184480205 none O=C(Nc1ncc(c2ccccc2)s1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 10, 10, 10, 10, 28, 28, 16, 28, 28, 10, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 10, 28, 28, 20, 28, 28, 9, 9, 9, 9] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480205 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480205/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480205 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 267) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/267: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ncc(c2ccccc2)s1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480205.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480205/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001184480205 none O=C(Nc1ncc(c2ccccc2)s1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 10, 10, 10, 10, 28, 28, 10, 28, 28, 10, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 10, 28, 28, 10, 28, 28, 9, 9, 9, 9] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480205 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184480205 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480205/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480205/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480205 Building ZINC001184480510 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480510' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480510 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480510 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480510/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480510 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 268) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/268 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/268' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(c2ccc(F)cc2)no1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480510.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480510/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001184480510 none O=C(Nc1cc(c2ccc(F)cc2)no1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 12, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 14, 14, 14, 29, 29, 17, 29, 29, 29, 14, 14, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 14, 29, 29, 29, 29, 9, 9, 9, 9] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480510 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480510/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480510 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 269) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/269 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/269' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(c2ccc(F)cc2)no1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480510.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480510/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001184480510 none O=C(Nc1cc(c2ccc(F)cc2)no1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 12, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 14, 14, 14, 30, 30, 19, 19, 30, 30, 14, 14, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 14, 30, 30, 30, 30, 9, 9, 9, 9] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480510 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184480510 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480510/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480510/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480510 Building ZINC001184480510 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480510' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480510 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480510 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480510/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480510 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 268) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/268: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(c2ccc(F)cc2)no1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480510.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480510/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001184480510 none O=C(Nc1cc(c2ccc(F)cc2)no1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 12, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 14, 14, 14, 29, 29, 17, 29, 29, 29, 14, 14, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 14, 29, 29, 29, 29, 9, 9, 9, 9] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480510 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480510/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480510 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 269) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/269: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(c2ccc(F)cc2)no1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480510.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480510/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001184480510 none O=C(Nc1cc(c2ccc(F)cc2)no1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 12, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 14, 14, 14, 30, 30, 19, 19, 30, 30, 14, 14, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 14, 30, 30, 30, 30, 9, 9, 9, 9] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480510 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184480510 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480510/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480510/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480510 Building ZINC001184480528 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480528' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480528 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480528 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480528/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480528 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 270) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/270 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/270' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H]1c1cc2ccccc2[nH]1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480528.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480528/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001184480528 none O=C(N1CCC[C@H]1c1cc2ccccc2[nH]1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 8, 6, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 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: [7, 1, 7, 12, 12, 12, 12, 12, 12, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 12, 12, 33, 33, 33, 33, 33, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480528 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480528/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480528 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 271) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/271 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/271' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H]1c1cc2ccccc2[nH]1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480528.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480528/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001184480528 none O=C(N1CCC[C@H]1c1cc2ccccc2[nH]1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 8, 6, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 6, 6, 6, 6, 6, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 19, 19, 19, 19, 19, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480528 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184480528 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480528/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480528/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480528 Building ZINC001184480528 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480528' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480528 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480528 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480528/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480528 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 270) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/270: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H]1c1cc2ccccc2[nH]1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480528.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480528/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001184480528 none O=C(N1CCC[C@H]1c1cc2ccccc2[nH]1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 8, 6, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 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: [7, 1, 7, 12, 12, 12, 12, 12, 12, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 12, 12, 33, 33, 33, 33, 33, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480528 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480528/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480528 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 271) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/271: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H]1c1cc2ccccc2[nH]1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480528.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480528/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001184480528 none O=C(N1CCC[C@H]1c1cc2ccccc2[nH]1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 8, 6, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 6, 6, 6, 6, 6, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 19, 19, 19, 19, 19, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480528 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184480528 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480528/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480528/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480528 Building ZINC001184480530 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480530' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480530 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480530 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480530/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480530 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 272) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/272 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/272' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H]1c1cc2ccccc2[nH]1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480530.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480530/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001184480530 none O=C(N1CCC[C@@H]1c1cc2ccccc2[nH]1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 8, 6, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 6, 6, 6, 6, 6, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 19, 19, 19, 19, 19, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480530 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480530/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480530 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 273) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/273 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/273' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H]1c1cc2ccccc2[nH]1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480530.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480530/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001184480530 none O=C(N1CCC[C@@H]1c1cc2ccccc2[nH]1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 8, 6, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 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: [7, 1, 7, 10, 10, 10, 10, 10, 10, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 10, 29, 29, 29, 29, 29, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480530 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184480530 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480530/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480530/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480530 Building ZINC001184480530 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480530' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480530 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480530 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480530/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480530 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 272) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/272: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H]1c1cc2ccccc2[nH]1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480530.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480530/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001184480530 none O=C(N1CCC[C@@H]1c1cc2ccccc2[nH]1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 8, 6, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 6, 6, 6, 6, 6, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 19, 19, 19, 19, 19, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480530 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480530/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480530 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 273) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/273: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H]1c1cc2ccccc2[nH]1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480530.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480530/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001184480530 none O=C(N1CCC[C@@H]1c1cc2ccccc2[nH]1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 8, 6, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 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: [7, 1, 7, 10, 10, 10, 10, 10, 10, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 10, 29, 29, 29, 29, 29, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480530 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184480530 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480530/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480530/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480530 Building ZINC001184480566 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480566' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480566 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480566 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480566/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480566 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 274) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/274 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/274' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(c2cccc(F)c2)ccn1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480566.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001184480566 none O=C(Nc1cc(c2cccc(F)c2)ccn1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 8, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 6, 21, 21, 21, 21, 21, 21, 6, 6, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 6, 21, 21, 21, 21, 6, 6, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480566 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480566/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480566 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 275) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/275 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/275' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(c2cccc(F)c2)ccn1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480566.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480566/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001184480566 none O=C(Nc1cc(c2cccc(F)c2)ccn1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 8, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 6, 21, 21, 21, 21, 21, 21, 6, 6, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 6, 21, 21, 21, 21, 6, 6, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480566 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184480566 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480566/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480566/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480566 Building ZINC001184480566 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480566' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480566 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480566 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480566/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480566 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 274) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/274: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(c2cccc(F)c2)ccn1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480566.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001184480566 none O=C(Nc1cc(c2cccc(F)c2)ccn1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 8, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 6, 21, 21, 21, 21, 21, 21, 6, 6, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 6, 21, 21, 21, 21, 6, 6, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480566 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480566/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480566 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 275) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/275: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(c2cccc(F)c2)ccn1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480566.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480566/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001184480566 none O=C(Nc1cc(c2cccc(F)c2)ccn1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 8, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 6, 21, 21, 21, 21, 21, 21, 6, 6, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 6, 21, 21, 21, 21, 6, 6, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480566 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184480566 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480566/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480566/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480566 Building ZINC001184480903 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480903' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480903 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480903 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480903/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480903 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 276) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/276 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/276' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(C=Cc3ccccc32)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480903.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480903/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001184480903 none O=C(N1CCC2(C=Cc3ccccc32)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480903 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480903/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480903 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 277) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/277 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/277' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(C=Cc3ccccc32)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480903.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480903/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001184480903 none O=C(N1CCC2(C=Cc3ccccc32)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480903 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184480903 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480903/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480903/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480903 Building ZINC001184480903 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480903' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480903 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480903 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480903/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480903 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 276) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/276: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(C=Cc3ccccc32)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480903.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480903/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001184480903 none O=C(N1CCC2(C=Cc3ccccc32)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480903 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480903/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480903 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 277) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/277: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(C=Cc3ccccc32)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480903.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480903/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001184480903 none O=C(N1CCC2(C=Cc3ccccc32)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480903 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184480903 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480903/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480903/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480903 Building ZINC001184480928 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480928' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480928 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480928 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480928/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480928 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 278) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/278 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/278' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H](Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480928.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480928/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001184480928 none O=C(N1CCC[C@@H](Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 8, 12, 12, 12, 12, 12, 12, 23, 23, 23, 23, 23, 23, 12, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 12, 23, 23, 23, 23, 23, 23, 23, 12, 12, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 86 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480928 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480928/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480928 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 279) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/279 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/279' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H](Cc2ccccc2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480928.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480928/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001184480928 none O=C(N1CCC[C@@H](Cc2ccccc2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 5, 9, 9, 9, 9, 9, 9, 19, 19, 19, 19, 19, 19, 9, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 19, 19, 19, 19, 19, 19, 19, 9, 9, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 78 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480928 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184480928 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480928/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480928/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480928 Building ZINC001184480928 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480928' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480928 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480928 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480928/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480928 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 278) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/278: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H](Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480928.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480928/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001184480928 none O=C(N1CCC[C@@H](Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 8, 12, 12, 12, 12, 12, 12, 23, 23, 23, 23, 23, 23, 12, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 12, 23, 23, 23, 23, 23, 23, 23, 12, 12, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 86 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480928 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480928/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480928 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 279) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/279: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H](Cc2ccccc2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480928.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480928/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001184480928 none O=C(N1CCC[C@@H](Cc2ccccc2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 5, 9, 9, 9, 9, 9, 9, 19, 19, 19, 19, 19, 19, 9, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 19, 19, 19, 19, 19, 19, 19, 9, 9, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 78 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480928 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184480928 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480928/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480928/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480928 Building ZINC001184480929 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480929' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480929 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480929 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480929/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480929 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 280) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/280 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/280' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H](Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480929.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480929/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001184480929 none O=C(N1CCC[C@H](Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 5, 10, 10, 10, 10, 10, 10, 21, 21, 21, 21, 21, 21, 10, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 10, 10, 10, 10, 21, 21, 21, 21, 21, 21, 21, 10, 10, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 83 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480929 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480929/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480929 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 281) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/281 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/281' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H](Cc2ccccc2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480929.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480929/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001184480929 none O=C(N1CCC[C@H](Cc2ccccc2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 8, 11, 11, 11, 11, 11, 11, 22, 22, 22, 22, 22, 22, 11, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 22, 22, 22, 22, 22, 22, 22, 11, 11, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 84 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480929 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184480929 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480929/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480929/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480929 Building ZINC001184480929 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480929' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480929 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480929 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480929/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480929 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 280) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/280: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H](Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480929.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480929/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001184480929 none O=C(N1CCC[C@H](Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 5, 10, 10, 10, 10, 10, 10, 21, 21, 21, 21, 21, 21, 10, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 10, 10, 10, 10, 21, 21, 21, 21, 21, 21, 21, 10, 10, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 83 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480929 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480929/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480929 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 281) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/281: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H](Cc2ccccc2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480929.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480929/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001184480929 none O=C(N1CCC[C@H](Cc2ccccc2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 8, 11, 11, 11, 11, 11, 11, 22, 22, 22, 22, 22, 22, 11, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 22, 22, 22, 22, 22, 22, 22, 11, 11, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 84 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480929 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184480929 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480929/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480929/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480929 Building ZINC001184480979 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480979' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480979 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480979 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480979/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480979 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 282) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/282 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/282' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)[C@@H](C)Cc1ccc(OC)cc1) `ZINC001184480979.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184480979 none CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)[C@@H](C)Cc1ccc(OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 15, 16, 16, 15, 15, 21, 16, 16, 8, 8, 8, 8, 8, 5, 5, 5, 5, 12, 12, 12, 15, 15, 16, 16, 21, 21, 21, 16, 16] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 98 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480979 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480979/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480979 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 283) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/283 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/283' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)[C@@H](C)Cc1ccc(OC)cc1) `ZINC001184480979.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480979/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184480979 none CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)[C@@H](C)Cc1ccc(OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 13, 13, 13, 19, 21, 21, 19, 21, 25, 21, 21, 7, 7, 7, 7, 7, 5, 5, 5, 5, 13, 13, 13, 19, 19, 21, 21, 25, 25, 25, 21, 21] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 107 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480979 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184480979 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480979/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480979/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480979 Building ZINC001184480979 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480979' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480979 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480979 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480979/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480979 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 282) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/282: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)[C@@H](C)Cc1ccc(OC)cc1) `ZINC001184480979.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184480979 none CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)[C@@H](C)Cc1ccc(OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 15, 16, 16, 15, 15, 21, 16, 16, 8, 8, 8, 8, 8, 5, 5, 5, 5, 12, 12, 12, 15, 15, 16, 16, 21, 21, 21, 16, 16] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 98 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480979 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480979/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480979 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 283) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/283: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)[C@@H](C)Cc1ccc(OC)cc1) `ZINC001184480979.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480979/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184480979 none CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)[C@@H](C)Cc1ccc(OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 13, 13, 13, 19, 21, 21, 19, 21, 25, 21, 21, 7, 7, 7, 7, 7, 5, 5, 5, 5, 13, 13, 13, 19, 19, 21, 21, 25, 25, 25, 21, 21] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 107 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480979 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184480979 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480979/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480979/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480979 Building ZINC001184480981 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480981' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480981 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480981 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480981/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480981 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 284) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/284 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/284' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)[C@H](C)Cc1ccc(OC)cc1) `ZINC001184480981.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480981/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184480981 none CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)[C@H](C)Cc1ccc(OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 13, 13, 13, 19, 21, 21, 21, 21, 25, 21, 21, 7, 7, 7, 7, 7, 5, 5, 5, 5, 13, 13, 13, 19, 19, 21, 21, 25, 25, 25, 21, 21] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 97 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480981 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480981/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480981 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 285) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/285 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/285' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)[C@H](C)Cc1ccc(OC)cc1) `ZINC001184480981.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480981/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184480981 none CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)[C@H](C)Cc1ccc(OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 15, 16, 16, 15, 16, 21, 16, 16, 8, 8, 8, 8, 8, 5, 5, 5, 5, 12, 12, 12, 15, 15, 16, 16, 21, 21, 21, 16, 16] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 100 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480981 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184480981 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480981/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480981/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480981 Building ZINC001184480981 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480981' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480981 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480981 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480981/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480981 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 284) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/284: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)[C@H](C)Cc1ccc(OC)cc1) `ZINC001184480981.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480981/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184480981 none CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)[C@H](C)Cc1ccc(OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 13, 13, 13, 19, 21, 21, 21, 21, 25, 21, 21, 7, 7, 7, 7, 7, 5, 5, 5, 5, 13, 13, 13, 19, 19, 21, 21, 25, 25, 25, 21, 21] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 97 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480981 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480981/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480981 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 285) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/285: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)[C@H](C)Cc1ccc(OC)cc1) `ZINC001184480981.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480981/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184480981 none CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)[C@H](C)Cc1ccc(OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 15, 16, 16, 15, 16, 21, 16, 16, 8, 8, 8, 8, 8, 5, 5, 5, 5, 12, 12, 12, 15, 15, 16, 16, 21, 21, 21, 16, 16] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 100 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480981 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184480981 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480981/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480981/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184480981 Building ZINC001184484401 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484401' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484401 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184484401 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484401/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484401 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 286) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/286 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/286' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cc2cc(Cl)ccc2[nH]1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484401.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001184484401 none O=C(NCc1cc2cc(Cl)ccc2[nH]1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 16, 1, 1, 1, 8, 6, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 21, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 21, 21, 31, 31, 31, 31, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484401 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484401/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484401 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 287) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/287 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/287' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cc2cc(Cl)ccc2[nH]1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484401.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484401/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001184484401 none O=C(NCc1cc2cc(Cl)ccc2[nH]1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 16, 1, 1, 1, 8, 6, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 20, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 20, 20, 29, 29, 29, 29, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484401 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184484401 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484401/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484401/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484401 Building ZINC001184484401 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484401' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484401 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184484401 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484401/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484401 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 286) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/286: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cc2cc(Cl)ccc2[nH]1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484401.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001184484401 none O=C(NCc1cc2cc(Cl)ccc2[nH]1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 16, 1, 1, 1, 8, 6, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 21, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 21, 21, 31, 31, 31, 31, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484401 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484401/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484401 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 287) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/287: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cc2cc(Cl)ccc2[nH]1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484401.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484401/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001184484401 none O=C(NCc1cc2cc(Cl)ccc2[nH]1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 16, 1, 1, 1, 8, 6, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 20, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 20, 20, 29, 29, 29, 29, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484401 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184484401 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484401/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484401/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484401 Building ZINC001184484431 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484431' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484431 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184484431 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484431/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484431 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 288) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/288 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/288' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc2cc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)c(C)cc2s1) `ZINC001184484431.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001184484431 none Cc1nc2cc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)c(C)cc2s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 5, 1, 1, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 6, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 6, 9, 9, 9, 9, 27, 27, 27, 27] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 49 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484431 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484431/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484431 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 289) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/289 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/289' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc2cc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)c(C)cc2s1) `ZINC001184484431.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484431/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001184484431 none Cc1nc2cc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)c(C)cc2s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 5, 1, 1, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 6, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 6, 9, 9, 9, 9, 27, 27, 27, 27] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 49 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484431 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184484431 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484431/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484431/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484431 Building ZINC001184484431 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484431' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484431 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184484431 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484431/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484431 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 288) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/288: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc2cc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)c(C)cc2s1) `ZINC001184484431.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001184484431 none Cc1nc2cc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)c(C)cc2s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 5, 1, 1, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 6, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 6, 9, 9, 9, 9, 27, 27, 27, 27] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 49 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484431 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484431/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484431 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 289) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/289: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc2cc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)c(C)cc2s1) `ZINC001184484431.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484431/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001184484431 none Cc1nc2cc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)c(C)cc2s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 5, 1, 1, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 6, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 6, 9, 9, 9, 9, 27, 27, 27, 27] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 49 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484431 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184484431 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484431/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484431/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484431 Building ZINC001184484720 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484720' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484720 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184484720 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484720/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484720 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 290) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/290 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/290' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(F)c(OCC2CC2)c(F)c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484720.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484720/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001184484720 none O=C(Nc1cc(F)c(OCC2CC2)c(F)c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 15, 1, 12, 5, 5, 5, 5, 1, 15, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 9, 9, 9, 9, 9, 14, 32, 39, 39, 9, 9, 9, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 9, 32, 32, 39, 39, 39, 39, 39, 9, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484720 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484720/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484720 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 291) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/291 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/291' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(F)c(OCC2CC2)c(F)c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484720.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484720/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001184484720 none O=C(Nc1cc(F)c(OCC2CC2)c(F)c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 15, 1, 12, 5, 5, 5, 5, 1, 15, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 5, 5, 5, 3, 3, 10, 31, 37, 37, 5, 5, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 5, 31, 31, 37, 37, 37, 37, 37, 5, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484720 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184484720 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484720/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484720/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484720 Building ZINC001184484720 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484720' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484720 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184484720 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484720/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484720 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 290) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/290: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(F)c(OCC2CC2)c(F)c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484720.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484720/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001184484720 none O=C(Nc1cc(F)c(OCC2CC2)c(F)c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 15, 1, 12, 5, 5, 5, 5, 1, 15, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 9, 9, 9, 9, 9, 14, 32, 39, 39, 9, 9, 9, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 9, 32, 32, 39, 39, 39, 39, 39, 9, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484720 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484720/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484720 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 291) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/291: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(F)c(OCC2CC2)c(F)c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484720.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484720/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001184484720 none O=C(Nc1cc(F)c(OCC2CC2)c(F)c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 15, 1, 12, 5, 5, 5, 5, 1, 15, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 5, 5, 5, 3, 3, 10, 31, 37, 37, 5, 5, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 5, 31, 31, 37, 37, 37, 37, 37, 5, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484720 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184484720 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484720/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484720/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484720 Building ZINC001184484713 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484713' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484713 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184484713 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484713/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484713 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 292) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/292 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/292' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1nc(c2ccccc2)cs1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484713.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001184484713 none O=C(NCc1nc(c2ccccc2)cs1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 12, 31, 31, 31, 41, 41, 38, 41, 41, 31, 31, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 41, 41, 40, 41, 41, 31, 3, 3, 3, 3] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484713 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484713/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484713 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 293) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/293 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/293' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1nc(c2ccccc2)cs1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484713.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484713/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001184484713 none O=C(NCc1nc(c2ccccc2)cs1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 12, 33, 33, 33, 40, 40, 33, 40, 40, 33, 33, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 40, 40, 34, 40, 40, 33, 3, 3, 3, 3] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484713 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184484713 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484713/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484713/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484713 Building ZINC001184484713 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484713' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484713 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184484713 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484713/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484713 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 292) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/292: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1nc(c2ccccc2)cs1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484713.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001184484713 none O=C(NCc1nc(c2ccccc2)cs1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 12, 31, 31, 31, 41, 41, 38, 41, 41, 31, 31, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 41, 41, 40, 41, 41, 31, 3, 3, 3, 3] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484713 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484713/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484713 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 293) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/293: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1nc(c2ccccc2)cs1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484713.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484713/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001184484713 none O=C(NCc1nc(c2ccccc2)cs1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 12, 33, 33, 33, 40, 40, 33, 40, 40, 33, 33, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 40, 40, 34, 40, 40, 33, 3, 3, 3, 3] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484713 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184484713 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484713/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484713/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484713 Building ZINC001184484769 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484769' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484769 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184484769 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484769/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484769 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 294) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/294 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/294' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc2c(Cl)ccnc12)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484769.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484769/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001184484769 none O=C(Nc1cccc2c(Cl)ccnc12)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 8, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 7, 22, 22, 22, 22, 22, 8, 8, 8, 8] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484769 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484769/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484769 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 295) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/295 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/295' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc2c(Cl)ccnc12)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484769.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484769/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001184484769 none O=C(Nc1cccc2c(Cl)ccnc12)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 8, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 7, 22, 22, 22, 22, 22, 8, 8, 8, 8] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484769 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184484769 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484769/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484769/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484769 Building ZINC001184484769 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484769' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484769 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184484769 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484769/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484769 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 294) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/294: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc2c(Cl)ccnc12)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484769.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484769/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001184484769 none O=C(Nc1cccc2c(Cl)ccnc12)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 8, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 7, 22, 22, 22, 22, 22, 8, 8, 8, 8] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484769 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484769/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484769 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 295) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/295: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc2c(Cl)ccnc12)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484769.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484769/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001184484769 none O=C(Nc1cccc2c(Cl)ccnc12)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 8, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 7, 22, 22, 22, 22, 22, 8, 8, 8, 8] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484769 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184484769 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484769/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484769/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484769 Building ZINC001184484947 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484947' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484947 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184484947 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484947/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484947 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 296) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/296 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/296' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)c1c[nH]c2ccccc21) `ZINC001184484947.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484947/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001184484947 none CC(C)(CNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)c1c[nH]c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 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, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 14, 18, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 19, 33, 33, 33, 33, 33, 33, 33, 33, 33, 19, 19, 19, 19, 19, 19, 14, 14, 3, 4, 4, 4, 4, 33, 33, 33, 33, 33] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484947 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484947/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484947 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 297) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/297 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/297' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CNC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)c1c[nH]c2ccccc21) `ZINC001184484947.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484947/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001184484947 none CC(C)(CNC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)c1c[nH]c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 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, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 14, 18, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 19, 33, 33, 33, 33, 33, 33, 33, 33, 33, 19, 19, 19, 19, 19, 19, 14, 14, 3, 4, 4, 4, 4, 33, 33, 33, 33, 33] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484947 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184484947 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484947/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484947/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484947 Building ZINC001184484947 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484947' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484947 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184484947 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484947/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484947 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 296) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/296: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)c1c[nH]c2ccccc21) `ZINC001184484947.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484947/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001184484947 none CC(C)(CNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)c1c[nH]c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 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, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 14, 18, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 19, 33, 33, 33, 33, 33, 33, 33, 33, 33, 19, 19, 19, 19, 19, 19, 14, 14, 3, 4, 4, 4, 4, 33, 33, 33, 33, 33] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484947 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484947/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484947 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 297) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/297: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CNC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)c1c[nH]c2ccccc21) `ZINC001184484947.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484947/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001184484947 none CC(C)(CNC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)c1c[nH]c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 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, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 14, 18, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 19, 33, 33, 33, 33, 33, 33, 33, 33, 33, 19, 19, 19, 19, 19, 19, 14, 14, 3, 4, 4, 4, 4, 33, 33, 33, 33, 33] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484947 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184484947 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484947/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484947/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184484947 Building ZINC001184485076 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184485076 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 298) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/298 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/298' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[C@H](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)CC1) `ZINC001184485076.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184485076 none C[N@]1CC[C@H](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 7, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 16, 25, 6, 12, 12, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 12, 12, 25, 25, 25, 25, 25, 25, 25, 25, 25, 12, 12, 3, 8, 8, 8, 8, 12, 12, 25, 25, 25, 25] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 299) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/299 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/299' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[C@@H](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)CC1) `ZINC001184485076.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184485076 none C[N@]1CC[C@@H](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 7, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 4, 25, 6, 12, 12, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 12, 12, 25, 25, 25, 25, 25, 25, 25, 25, 25, 12, 12, 3, 8, 8, 8, 8, 12, 12, 25, 25, 25, 25] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 300) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/300 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/300' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[C@H](c2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)CC1) `ZINC001184485076.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184485076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184485076 none C[N@]1CC[C@H](c2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 7, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 4, 25, 3, 12, 12, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 12, 12, 25, 25, 25, 25, 25, 25, 25, 25, 25, 12, 12, 3, 8, 8, 8, 8, 12, 12, 25, 25, 25, 25] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 301) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/301 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/301' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[C@@H](c2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)CC1) `ZINC001184485076.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184485076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184485076 none C[N@]1CC[C@@H](c2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 7, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 4, 25, 3, 12, 12, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 12, 12, 25, 25, 25, 25, 25, 25, 25, 25, 25, 12, 12, 3, 8, 8, 8, 8, 12, 12, 25, 25, 25, 25] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184485076 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076 Building ZINC001184485076 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184485076 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 298) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/298: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[C@H](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)CC1) `ZINC001184485076.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184485076 none C[N@]1CC[C@H](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 7, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 16, 25, 6, 12, 12, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 12, 12, 25, 25, 25, 25, 25, 25, 25, 25, 25, 12, 12, 3, 8, 8, 8, 8, 12, 12, 25, 25, 25, 25] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 299) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/299: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[C@@H](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)CC1) `ZINC001184485076.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184485076 none C[N@]1CC[C@@H](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 7, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 4, 25, 6, 12, 12, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 12, 12, 25, 25, 25, 25, 25, 25, 25, 25, 25, 12, 12, 3, 8, 8, 8, 8, 12, 12, 25, 25, 25, 25] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 300) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/300: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[C@H](c2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)CC1) `ZINC001184485076.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184485076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184485076 none C[N@]1CC[C@H](c2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 7, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 4, 25, 3, 12, 12, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 12, 12, 25, 25, 25, 25, 25, 25, 25, 25, 25, 12, 12, 3, 8, 8, 8, 8, 12, 12, 25, 25, 25, 25] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 301) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/301: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[C@@H](c2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)CC1) `ZINC001184485076.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184485076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184485076 none C[N@]1CC[C@@H](c2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 7, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 4, 25, 3, 12, 12, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 12, 12, 25, 25, 25, 25, 25, 25, 25, 25, 25, 12, 12, 3, 8, 8, 8, 8, 12, 12, 25, 25, 25, 25] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184485076 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076 Building ZINC001184485076 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184485076 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 298) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/298: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[C@H](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)CC1) `ZINC001184485076.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184485076 none C[N@]1CC[C@H](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 7, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 16, 25, 6, 12, 12, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 12, 12, 25, 25, 25, 25, 25, 25, 25, 25, 25, 12, 12, 3, 8, 8, 8, 8, 12, 12, 25, 25, 25, 25] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 299) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/299: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[C@@H](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)CC1) `ZINC001184485076.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184485076 none C[N@]1CC[C@@H](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 7, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 4, 25, 6, 12, 12, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 12, 12, 25, 25, 25, 25, 25, 25, 25, 25, 25, 12, 12, 3, 8, 8, 8, 8, 12, 12, 25, 25, 25, 25] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 300) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/300: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[C@H](c2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)CC1) `ZINC001184485076.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184485076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184485076 none C[N@]1CC[C@H](c2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 7, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 4, 25, 3, 12, 12, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 12, 12, 25, 25, 25, 25, 25, 25, 25, 25, 25, 12, 12, 3, 8, 8, 8, 8, 12, 12, 25, 25, 25, 25] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 301) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/301: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[C@@H](c2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)CC1) `ZINC001184485076.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184485076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184485076 none C[N@]1CC[C@@H](c2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 7, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 4, 25, 3, 12, 12, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 12, 12, 25, 25, 25, 25, 25, 25, 25, 25, 25, 12, 12, 3, 8, 8, 8, 8, 12, 12, 25, 25, 25, 25] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184485076 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076 Building ZINC001184485076 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184485076 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 298) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/298: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[C@H](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)CC1) `ZINC001184485076.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184485076 none C[N@]1CC[C@H](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 7, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 16, 25, 6, 12, 12, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 12, 12, 25, 25, 25, 25, 25, 25, 25, 25, 25, 12, 12, 3, 8, 8, 8, 8, 12, 12, 25, 25, 25, 25] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 299) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/299: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[C@@H](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)CC1) `ZINC001184485076.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184485076 none C[N@]1CC[C@@H](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 7, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 4, 25, 6, 12, 12, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 12, 12, 25, 25, 25, 25, 25, 25, 25, 25, 25, 12, 12, 3, 8, 8, 8, 8, 12, 12, 25, 25, 25, 25] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 300) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/300: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[C@H](c2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)CC1) `ZINC001184485076.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184485076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184485076 none C[N@]1CC[C@H](c2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 7, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 4, 25, 3, 12, 12, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 12, 12, 25, 25, 25, 25, 25, 25, 25, 25, 25, 12, 12, 3, 8, 8, 8, 8, 12, 12, 25, 25, 25, 25] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 301) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/301: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[C@@H](c2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)CC1) `ZINC001184485076.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184485076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184485076 none C[N@]1CC[C@@H](c2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 7, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 4, 25, 3, 12, 12, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 12, 12, 25, 25, 25, 25, 25, 25, 25, 25, 25, 12, 12, 3, 8, 8, 8, 8, 12, 12, 25, 25, 25, 25] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184485076 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485076 Building ZINC001184485096 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485096' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485096 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485096 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485096/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485096 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 302) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/302 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/302' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNc1ccc(C(F)(F)F)cc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485096.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001184485096 none CNc1ccc(C(F)(F)F)cc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 16, 16, 16, 9, 16, 16, 16, 16, 16, 16, 5, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 21, 21, 21, 21, 16, 16, 16, 5, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485096 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485096/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485096 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 303) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/303 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/303' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNc1ccc(C(F)(F)F)cc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485096.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485096/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001184485096 none CNc1ccc(C(F)(F)F)cc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 16, 9, 16, 16, 16, 16, 16, 16, 5, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 20, 20, 20, 20, 16, 16, 16, 5, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485096 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184485096 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485096/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485096/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485096 Building ZINC001184485096 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485096' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485096 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485096 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485096/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485096 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 302) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/302: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNc1ccc(C(F)(F)F)cc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485096.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001184485096 none CNc1ccc(C(F)(F)F)cc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 16, 16, 16, 9, 16, 16, 16, 16, 16, 16, 5, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 21, 21, 21, 21, 16, 16, 16, 5, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485096 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485096/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485096 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 303) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/303: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNc1ccc(C(F)(F)F)cc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485096.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485096/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001184485096 none CNc1ccc(C(F)(F)F)cc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 16, 9, 16, 16, 16, 16, 16, 16, 5, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 20, 20, 20, 20, 16, 16, 16, 5, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485096 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184485096 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485096/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485096/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485096 Building ZINC001184485172 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485172' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485172 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485172 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485172/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485172 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 304) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/304 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/304' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2nc(S)sc2c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485172.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485172/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001184485172 none O=C(Nc1ccc2nc(S)sc2c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'S.3', 'S.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 14, 14, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 23, 23, 69, 23, 9, 9, 9, 9] 150 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485172 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485172/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485172 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 305) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/305 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/305' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2nc(S)sc2c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485172.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485172/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001184485172 none O=C(Nc1ccc2nc(S)sc2c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'S.3', 'S.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 14, 14, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 22, 22, 66, 22, 9, 9, 9, 9] 150 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485172 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184485172 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485172/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485172/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485172 Building ZINC001184485172 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485172' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485172 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485172 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485172/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485172 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 304) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/304: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2nc(S)sc2c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485172.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485172/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001184485172 none O=C(Nc1ccc2nc(S)sc2c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'S.3', 'S.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 14, 14, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 23, 23, 69, 23, 9, 9, 9, 9] 150 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485172 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485172/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485172 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 305) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/305: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2nc(S)sc2c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485172.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485172/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001184485172 none O=C(Nc1ccc2nc(S)sc2c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'S.3', 'S.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 14, 14, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 22, 22, 66, 22, 9, 9, 9, 9] 150 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485172 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184485172 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485172/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485172/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485172 Building ZINC001184485187 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485187' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485187 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485187 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485187/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485187 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 306) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/306 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/306' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H]1c1ccc(F)cc1F)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485187.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485187/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001184485187 none O=C(N1CCC[C@@H]1c1ccc(F)cc1F)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 10, 10, 10, 10, 10, 10, 18, 18, 17, 18, 18, 18, 18, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 10, 10, 10, 10, 18, 18, 18, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485187 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485187/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485187 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 307) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/307 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/307' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H]1c1ccc(F)cc1F)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485187.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485187/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001184485187 none O=C(N1CCC[C@@H]1c1ccc(F)cc1F)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 13, 13, 13, 13, 13, 13, 23, 23, 13, 23, 23, 23, 23, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 13, 13, 13, 13, 13, 13, 23, 23, 23, 7, 7, 7, 7] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485187 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184485187 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485187/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485187/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485187 Building ZINC001184485187 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485187' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485187 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485187 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485187/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485187 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 306) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/306: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H]1c1ccc(F)cc1F)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485187.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485187/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001184485187 none O=C(N1CCC[C@@H]1c1ccc(F)cc1F)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 10, 10, 10, 10, 10, 10, 18, 18, 17, 18, 18, 18, 18, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 10, 10, 10, 10, 18, 18, 18, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485187 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485187/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485187 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 307) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/307: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H]1c1ccc(F)cc1F)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485187.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485187/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001184485187 none O=C(N1CCC[C@@H]1c1ccc(F)cc1F)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 13, 13, 13, 13, 13, 13, 23, 23, 13, 23, 23, 23, 23, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 13, 13, 13, 13, 13, 13, 23, 23, 23, 7, 7, 7, 7] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485187 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184485187 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485187/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485187/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485187 Building ZINC001184485189 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485189' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485189 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485189 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485189/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485189 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 308) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/308 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/308' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H]1c1ccc(F)cc1F)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485189.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485189/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001184485189 none O=C(N1CCC[C@H]1c1ccc(F)cc1F)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 14, 14, 14, 14, 14, 14, 21, 21, 19, 21, 21, 21, 21, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 21, 21, 21, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485189 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485189/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485189 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 309) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/309 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/309' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H]1c1ccc(F)cc1F)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485189.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485189/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001184485189 none O=C(N1CCC[C@H]1c1ccc(F)cc1F)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 10, 10, 10, 10, 10, 10, 18, 18, 15, 18, 18, 18, 18, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 10, 10, 10, 10, 18, 18, 18, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485189 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184485189 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485189/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485189/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485189 Building ZINC001184485189 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485189' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485189 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485189 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485189/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485189 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 308) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/308: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H]1c1ccc(F)cc1F)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485189.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485189/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001184485189 none O=C(N1CCC[C@H]1c1ccc(F)cc1F)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 14, 14, 14, 14, 14, 14, 21, 21, 19, 21, 21, 21, 21, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 21, 21, 21, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485189 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485189/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485189 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 309) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/309: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H]1c1ccc(F)cc1F)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485189.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485189/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001184485189 none O=C(N1CCC[C@H]1c1ccc(F)cc1F)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 10, 10, 10, 10, 10, 10, 18, 18, 15, 18, 18, 18, 18, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 10, 10, 10, 10, 18, 18, 18, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485189 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184485189 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485189/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485189/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485189 Building ZINC001184485586 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485586' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485586 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485586 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485586/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485586 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 310) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/310 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/310' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccccn1)C1CCCCC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485586.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485586/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001184485586 none O=C(N(Cc1ccccn1)C1CCCCC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 7, 15, 21, 21, 21, 21, 21, 7, 11, 11, 11, 11, 11, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 15, 15, 21, 21, 21, 21, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 86 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485586 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485586/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485586 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 311) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/311 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/311' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccccn1)C1CCCCC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485586.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485586/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001184485586 none O=C(N(Cc1ccccn1)C1CCCCC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 13, 20, 20, 20, 20, 20, 6, 10, 10, 10, 10, 10, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 20, 20, 20, 20, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 80 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485586 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184485586 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485586/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485586/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485586 Building ZINC001184485586 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485586' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485586 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485586 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485586/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485586 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 310) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/310: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccccn1)C1CCCCC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485586.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485586/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001184485586 none O=C(N(Cc1ccccn1)C1CCCCC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 7, 15, 21, 21, 21, 21, 21, 7, 11, 11, 11, 11, 11, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 15, 15, 21, 21, 21, 21, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 86 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485586 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485586/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485586 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 311) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/311: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccccn1)C1CCCCC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485586.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485586/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001184485586 none O=C(N(Cc1ccccn1)C1CCCCC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 13, 20, 20, 20, 20, 20, 6, 10, 10, 10, 10, 10, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 20, 20, 20, 20, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 80 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485586 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184485586 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485586/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485586/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485586 Building ZINC001184485641 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485641' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485641 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485641 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485641/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485641 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 312) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/312 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/312' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1c(Cl)ccc2ncccc21)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485641.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485641/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001184485641 none O=C(Nc1c(Cl)ccc2ncccc21)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 16, 1, 1, 1, 8, 1, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 20, 20, 20, 20, 20, 8, 8, 8, 8] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 38 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485641 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485641/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485641 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 313) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/313 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/313' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1c(Cl)ccc2ncccc21)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485641.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485641/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001184485641 none O=C(Nc1c(Cl)ccc2ncccc21)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 16, 1, 1, 1, 8, 1, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 20, 20, 20, 20, 20, 8, 8, 8, 8] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 38 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485641 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184485641 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485641/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485641/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485641 Building ZINC001184485641 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485641' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485641 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485641 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485641/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485641 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 312) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/312: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1c(Cl)ccc2ncccc21)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485641.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485641/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001184485641 none O=C(Nc1c(Cl)ccc2ncccc21)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 16, 1, 1, 1, 8, 1, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 20, 20, 20, 20, 20, 8, 8, 8, 8] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 38 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485641 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485641/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485641 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 313) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/313: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1c(Cl)ccc2ncccc21)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485641.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485641/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001184485641 none O=C(Nc1c(Cl)ccc2ncccc21)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 16, 1, 1, 1, 8, 1, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 20, 20, 20, 20, 20, 8, 8, 8, 8] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 38 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485641 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184485641 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485641/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485641/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485641 Building ZINC001184485693 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485693' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485693 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485693 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485693/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485693 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 314) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/314 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/314' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccccc1c1nccs1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485693.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485693/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001184485693 none O=C(Nc1ccccc1c1nccs1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 14, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 8, 8, 8, 8, 24, 24, 24, 24, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 8, 8, 8, 8, 24, 24, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485693 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485693/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485693 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 315) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/315 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/315' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccccc1c1nccs1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485693.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485693/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001184485693 none O=C(Nc1ccccc1c1nccs1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 14, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 8, 8, 8, 8, 23, 23, 23, 23, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 8, 8, 8, 8, 23, 23, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485693 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184485693 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485693/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485693/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485693 Building ZINC001184485693 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485693' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485693 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485693 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485693/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485693 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 314) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/314: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccccc1c1nccs1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485693.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485693/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001184485693 none O=C(Nc1ccccc1c1nccs1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 14, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 8, 8, 8, 8, 24, 24, 24, 24, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 8, 8, 8, 8, 24, 24, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485693 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485693/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485693 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 315) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/315: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccccc1c1nccs1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485693.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485693/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001184485693 none O=C(Nc1ccccc1c1nccs1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 14, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 8, 8, 8, 8, 23, 23, 23, 23, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 8, 8, 8, 8, 23, 23, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485693 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184485693 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485693/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485693/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184485693 Building ZINC001184486237 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486237' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486237 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486237 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486237/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486237 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 316) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/316 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/316' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc2cc(Cl)c(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2o1) `ZINC001184486237.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486237/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001184486237 none Cc1nc2cc(Cl)c(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 25, 25, 6, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 25, 25, 25, 25, 25, 25, 25, 6, 9, 9, 9, 9, 25] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 47 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486237 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486237/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486237 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 317) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/317 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/317' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc2cc(Cl)c(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2o1) `ZINC001184486237.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486237/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001184486237 none Cc1nc2cc(Cl)c(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 6, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 26, 26, 26, 26, 26, 26, 26, 6, 9, 9, 9, 9, 26] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486237 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184486237 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486237/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486237/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486237 Building ZINC001184486237 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486237' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486237 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486237 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486237/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486237 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 316) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/316: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc2cc(Cl)c(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2o1) `ZINC001184486237.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486237/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001184486237 none Cc1nc2cc(Cl)c(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 25, 25, 6, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 25, 25, 25, 25, 25, 25, 25, 6, 9, 9, 9, 9, 25] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 47 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486237 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486237/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486237 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 317) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/317: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc2cc(Cl)c(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2o1) `ZINC001184486237.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486237/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001184486237 none Cc1nc2cc(Cl)c(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 6, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 26, 26, 26, 26, 26, 26, 26, 6, 9, 9, 9, 9, 26] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486237 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184486237 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486237/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486237/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486237 Building ZINC001184486305 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486305' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486305 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486305 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486305/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486305 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 318) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/318 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/318' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1c(Cl)ccc(O)c1Cl)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486305.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001184486305 none O=C(Nc1c(Cl)ccc(O)c1Cl)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 16, 1, 1, 1, 12, 1, 16, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 8, 10, 11, 7, 4, 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: [6, 1, 6, 6, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 25, 25, 50, 8, 8, 8, 8] 100 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486305 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486305/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486305 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 319) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/319 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/319' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1c(Cl)ccc(O)c1Cl)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486305.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486305/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001184486305 none O=C(Nc1c(Cl)ccc(O)c1Cl)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 16, 1, 1, 1, 12, 1, 16, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 8, 10, 11, 7, 4, 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: [6, 1, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 27, 27, 54, 8, 8, 8, 8] 100 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486305 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184486305 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486305/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486305/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486305 Building ZINC001184486305 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486305' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486305 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486305 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486305/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486305 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 318) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/318: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1c(Cl)ccc(O)c1Cl)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486305.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001184486305 none O=C(Nc1c(Cl)ccc(O)c1Cl)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 16, 1, 1, 1, 12, 1, 16, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 8, 10, 11, 7, 4, 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: [6, 1, 6, 6, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 25, 25, 50, 8, 8, 8, 8] 100 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486305 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486305/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486305 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 319) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/319: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1c(Cl)ccc(O)c1Cl)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486305.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486305/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001184486305 none O=C(Nc1c(Cl)ccc(O)c1Cl)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 16, 1, 1, 1, 12, 1, 16, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 8, 10, 11, 7, 4, 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: [6, 1, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 27, 27, 54, 8, 8, 8, 8] 100 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486305 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184486305 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486305/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486305/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486305 Building ZINC001184486323 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486323' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486323 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486323 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486323/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486323 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 320) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/320 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/320' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](c2ccccc2)C(F)(F)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486323.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486323/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001184486323 none O=C(N1CC[C@@H](c2ccccc2)C(F)(F)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 2, 15, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 6, 6, 6] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 44 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486323 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486323/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486323 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 321) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/321 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/321' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](c2ccccc2)C(F)(F)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486323.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486323/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001184486323 none O=C(N1CC[C@@H](c2ccccc2)C(F)(F)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 6, 6, 6] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 39 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486323 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184486323 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486323/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486323/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486323 Building ZINC001184486323 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486323' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486323 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486323 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486323/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486323 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 320) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/320: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](c2ccccc2)C(F)(F)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486323.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486323/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001184486323 none O=C(N1CC[C@@H](c2ccccc2)C(F)(F)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 2, 15, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 6, 6, 6] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 44 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486323 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486323/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486323 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 321) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/321: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](c2ccccc2)C(F)(F)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486323.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486323/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001184486323 none O=C(N1CC[C@@H](c2ccccc2)C(F)(F)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 6, 6, 6] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 39 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486323 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184486323 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486323/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486323/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486323 Building ZINC001184486324 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486324' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486324 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486324 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486324/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486324 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 322) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/322 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/322' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](c2ccccc2)C(F)(F)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486324.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486324/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001184486324 none O=C(N1CC[C@H](c2ccccc2)C(F)(F)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 6, 6, 6] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 43 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486324 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486324/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486324 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 323) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/323 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/323' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](c2ccccc2)C(F)(F)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486324.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486324/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001184486324 none O=C(N1CC[C@H](c2ccccc2)C(F)(F)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 21, 21, 21, 21, 21, 22, 22, 21, 22, 22, 21, 21, 21, 21, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 21, 22, 22, 21, 22, 22, 21, 21, 6, 6, 6, 6] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 49 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486324 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184486324 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486324/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486324/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486324 Building ZINC001184486324 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486324' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486324 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486324 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486324/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486324 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 322) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/322: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](c2ccccc2)C(F)(F)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486324.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486324/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001184486324 none O=C(N1CC[C@H](c2ccccc2)C(F)(F)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 6, 6, 6] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 43 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486324 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486324/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486324 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 323) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/323: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](c2ccccc2)C(F)(F)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486324.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486324/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001184486324 none O=C(N1CC[C@H](c2ccccc2)C(F)(F)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 21, 21, 21, 21, 21, 22, 22, 21, 22, 22, 21, 21, 21, 21, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 21, 22, 22, 21, 22, 22, 21, 21, 6, 6, 6, 6] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 49 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486324 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184486324 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486324/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486324/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486324 Building ZINC001184486645 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486645' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486645 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486645 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486645/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486645 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 324) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/324 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/324' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccnc3Oc3ccc(C)c4c3CCC4)c2c1) `ZINC001184486645.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486645/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184486645 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccnc3Oc3ccc(C)c4c3CCC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 12, 1, 1, 1, 1, 5, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 6, 16, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 4, 4, 4, 4, 4, 4, 4, 3, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486645 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486645/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486645 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 325) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/325 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/325' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccnc3Oc3ccc(C)c4c3CCC4)c2c1) `ZINC001184486645.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486645/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184486645 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccnc3Oc3ccc(C)c4c3CCC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 12, 1, 1, 1, 1, 5, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 13, 24, 24, 24, 24, 24, 24, 24, 24, 24, 4, 4, 4, 4, 4, 4, 4, 4, 3, 5, 5, 5, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486645 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184486645 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486645/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486645/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486645 Building ZINC001184486645 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486645' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486645 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486645 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486645/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486645 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 324) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/324: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccnc3Oc3ccc(C)c4c3CCC4)c2c1) `ZINC001184486645.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486645/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184486645 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccnc3Oc3ccc(C)c4c3CCC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 12, 1, 1, 1, 1, 5, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 6, 16, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 4, 4, 4, 4, 4, 4, 4, 3, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486645 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486645/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486645 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 325) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/325: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccnc3Oc3ccc(C)c4c3CCC4)c2c1) `ZINC001184486645.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486645/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184486645 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccnc3Oc3ccc(C)c4c3CCC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 12, 1, 1, 1, 1, 5, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 13, 24, 24, 24, 24, 24, 24, 24, 24, 24, 4, 4, 4, 4, 4, 4, 4, 4, 3, 5, 5, 5, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486645 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184486645 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486645/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486645/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486645 Building ZINC001184486660 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486660' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486660 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486660 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486660/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486660 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 326) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/326 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/326' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cc(c4cccc(C(F)(F)F)c4)no3)c2c1) `ZINC001184486660.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486660/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001184486660 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cc(c4cccc(C(F)(F)F)c4)no3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 32, 32, 9, 32, 32, 32, 32, 32, 32, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 3, 9, 32, 32, 9, 32, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486660 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486660/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486660 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 327) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/327 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/327' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cc(c4cccc(C(F)(F)F)c4)no3)c2c1) `ZINC001184486660.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486660/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001184486660 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cc(c4cccc(C(F)(F)F)c4)no3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 32, 32, 9, 32, 32, 32, 32, 32, 32, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 3, 9, 32, 32, 9, 32, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486660 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184486660 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486660/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486660/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486660 Building ZINC001184486660 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486660' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486660 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486660 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486660/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486660 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 326) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/326: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cc(c4cccc(C(F)(F)F)c4)no3)c2c1) `ZINC001184486660.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486660/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001184486660 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cc(c4cccc(C(F)(F)F)c4)no3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 32, 32, 9, 32, 32, 32, 32, 32, 32, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 3, 9, 32, 32, 9, 32, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486660 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486660/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486660 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 327) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/327: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cc(c4cccc(C(F)(F)F)c4)no3)c2c1) `ZINC001184486660.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486660/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001184486660 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cc(c4cccc(C(F)(F)F)c4)no3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 32, 32, 9, 32, 32, 32, 32, 32, 32, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 3, 9, 32, 32, 9, 32, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486660 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184486660 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486660/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486660/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486660 Building ZINC001184486667 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486667' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486667 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486667 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486667/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486667 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 328) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/328 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/328' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3sc(C)c(C)c3C(=O)c3ccccc3)c2c1) `ZINC001184486667.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486667/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184486667 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3sc(C)c(C)c3C(=O)c3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 5, 1, 5, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 10, 10, 10, 10, 16, 16, 16, 16, 16, 16, 16, 8, 8, 8, 8, 8, 8, 8, 8, 5, 10, 10, 10, 10, 10, 10, 16, 16, 16, 16, 16, 8] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 51 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486667 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486667/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486667 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 329) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/329 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/329' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3sc(C)c(C)c3C(=O)c3ccccc3)c2c1) `ZINC001184486667.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486667/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184486667 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3sc(C)c(C)c3C(=O)c3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 5, 1, 5, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 8, 8, 8, 8, 8, 4, 12, 12, 12, 12, 12, 12, 17, 17, 17, 17, 17, 8] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 48 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486667 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184486667 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486667/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486667/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486667 Building ZINC001184486667 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486667' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486667 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486667 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486667/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486667 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 328) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/328: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3sc(C)c(C)c3C(=O)c3ccccc3)c2c1) `ZINC001184486667.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486667/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184486667 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3sc(C)c(C)c3C(=O)c3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 5, 1, 5, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 10, 10, 10, 10, 16, 16, 16, 16, 16, 16, 16, 8, 8, 8, 8, 8, 8, 8, 8, 5, 10, 10, 10, 10, 10, 10, 16, 16, 16, 16, 16, 8] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 51 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486667 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486667/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486667 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 329) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/329: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3sc(C)c(C)c3C(=O)c3ccccc3)c2c1) `ZINC001184486667.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486667/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184486667 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3sc(C)c(C)c3C(=O)c3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 5, 1, 5, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 8, 8, 8, 8, 8, 4, 12, 12, 12, 12, 12, 12, 17, 17, 17, 17, 17, 8] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 48 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486667 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184486667 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486667/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486667/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486667 Building ZINC001184486757 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486757' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486757 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486757 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486757/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486757 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 330) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/330 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/330' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1c[nH]c2cccc(Cl)c12)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486757.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001184486757 none O=C(NCCc1c[nH]c2cccc(Cl)c12)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 16, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 15, 25, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 15, 15, 25, 25, 26, 26, 26, 26, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486757 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486757/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486757 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 331) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/331 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/331' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1c[nH]c2cccc(Cl)c12)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486757.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486757/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001184486757 none O=C(NCCc1c[nH]c2cccc(Cl)c12)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 16, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 15, 25, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 15, 15, 25, 25, 26, 26, 26, 26, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486757 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184486757 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486757/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486757/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486757 Building ZINC001184486757 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486757' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486757 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486757 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486757/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486757 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 330) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/330: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1c[nH]c2cccc(Cl)c12)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486757.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001184486757 none O=C(NCCc1c[nH]c2cccc(Cl)c12)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 16, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 15, 25, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 15, 15, 25, 25, 26, 26, 26, 26, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486757 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486757/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486757 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 331) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/331: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1c[nH]c2cccc(Cl)c12)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486757.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486757/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001184486757 none O=C(NCCc1c[nH]c2cccc(Cl)c12)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 16, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 15, 25, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 15, 15, 25, 25, 26, 26, 26, 26, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486757 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184486757 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486757/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486757/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486757 Building ZINC001184486800 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486800' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486800 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486800 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486800/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486800 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 332) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/332 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/332' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c2ccccc12) `ZINC001184486800.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486800/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001184486800 none COc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 26, 26, 26, 26, 14, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 26, 26, 26, 26, 26, 26, 30, 30, 30, 26, 26, 14, 14, 3, 4, 4, 4, 4, 26, 26, 26, 26] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486800 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486800/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486800 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 333) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/333 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/333' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c2ccccc12) `ZINC001184486800.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486800/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001184486800 none COc1ccc(CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 27, 27, 27, 27, 15, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27, 27, 27, 30, 30, 30, 27, 27, 15, 15, 3, 4, 4, 4, 4, 27, 27, 27, 27] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486800 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184486800 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486800/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486800/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486800 Building ZINC001184486800 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486800' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486800 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486800 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486800/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486800 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 332) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/332: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c2ccccc12) `ZINC001184486800.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486800/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001184486800 none COc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 26, 26, 26, 26, 14, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 26, 26, 26, 26, 26, 26, 30, 30, 30, 26, 26, 14, 14, 3, 4, 4, 4, 4, 26, 26, 26, 26] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486800 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486800/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486800 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 333) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/333: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c2ccccc12) `ZINC001184486800.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486800/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001184486800 none COc1ccc(CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 27, 27, 27, 27, 15, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27, 27, 27, 30, 30, 30, 27, 27, 15, 15, 3, 4, 4, 4, 4, 27, 27, 27, 27] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486800 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184486800 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486800/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486800/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486800 Building ZINC001184486959 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486959' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486959 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486959 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486959/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486959 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 334) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/334 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/334' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(F)cc(Br)c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486959.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486959/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001184486959 none O=C(Nc1cc(F)cc(Br)c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 15, 1, 1, 17, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 22, 22, 22, 9, 9, 9, 9] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486959 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486959/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486959 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 335) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/335 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/335' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(F)cc(Br)c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486959.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486959/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001184486959 none O=C(Nc1cc(F)cc(Br)c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 15, 1, 1, 17, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 22, 22, 22, 9, 9, 9, 9] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486959 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184486959 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486959/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486959/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486959 Building ZINC001184486959 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486959' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486959 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486959 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486959/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486959 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 334) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/334: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(F)cc(Br)c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486959.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486959/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001184486959 none O=C(Nc1cc(F)cc(Br)c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 15, 1, 1, 17, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 22, 22, 22, 9, 9, 9, 9] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486959 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486959/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486959 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 335) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/335: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(F)cc(Br)c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486959.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486959/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001184486959 none O=C(Nc1cc(F)cc(Br)c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 15, 1, 1, 17, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 22, 22, 22, 9, 9, 9, 9] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486959 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184486959 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486959/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486959/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184486959 Building ZINC001184487000 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487000' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487000 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487000 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487000/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487000 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 336) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/336 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/336' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C(F)(F)F)ccc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487000.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487000/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001184487000 none COc1cc(C(F)(F)F)ccc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 27, 27, 27, 20, 20, 20, 6, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487000 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487000/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487000 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 337) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/337 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/337' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C(F)(F)F)ccc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487000.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487000/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001184487000 none COc1cc(C(F)(F)F)ccc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 27, 27, 27, 20, 20, 20, 6, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487000 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184487000 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487000/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487000/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487000 Building ZINC001184487000 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487000' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487000 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487000 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487000/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487000 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 336) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/336: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C(F)(F)F)ccc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487000.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487000/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001184487000 none COc1cc(C(F)(F)F)ccc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 27, 27, 27, 20, 20, 20, 6, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487000 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487000/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487000 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 337) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/337: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C(F)(F)F)ccc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487000.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487000/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001184487000 none COc1cc(C(F)(F)F)ccc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 27, 27, 27, 20, 20, 20, 6, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487000 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184487000 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487000/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487000/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487000 Building ZINC001184487029 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487029' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487029 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487029 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487029/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487029 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 338) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/338 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/338' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1ccc2c(c1)Cc1cc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)ccc1-2) `ZINC001184487029.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487029/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001184487029 none Nc1ccc2c(c1)Cc1cc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)ccc1-2 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 5, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 22, 22, 16, 22, 22, 22, 22, 22, 22, 22, 22, 5, 9, 9, 9, 9, 22, 22] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487029 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487029/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487029 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 339) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/339 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/339' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1ccc2c(c1)Cc1cc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)ccc1-2) `ZINC001184487029.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487029/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001184487029 none Nc1ccc2c(c1)Cc1cc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)ccc1-2 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 5, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 22, 22, 10, 22, 22, 22, 22, 22, 22, 22, 22, 5, 9, 9, 9, 9, 22, 22] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487029 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184487029 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487029/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487029/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487029 Building ZINC001184487029 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487029' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487029 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487029 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487029/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487029 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 338) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/338: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1ccc2c(c1)Cc1cc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)ccc1-2) `ZINC001184487029.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487029/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001184487029 none Nc1ccc2c(c1)Cc1cc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)ccc1-2 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 5, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 22, 22, 16, 22, 22, 22, 22, 22, 22, 22, 22, 5, 9, 9, 9, 9, 22, 22] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487029 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487029/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487029 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 339) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/339: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1ccc2c(c1)Cc1cc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)ccc1-2) `ZINC001184487029.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487029/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001184487029 none Nc1ccc2c(c1)Cc1cc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)ccc1-2 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 5, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 22, 22, 10, 22, 22, 22, 22, 22, 22, 22, 22, 5, 9, 9, 9, 9, 22, 22] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487029 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184487029 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487029/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487029/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487029 Building ZINC001184487615 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487615' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487615 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487615 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487615/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487615 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 340) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/340 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/340' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(OCC(F)(F)F)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487615.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487615/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001184487615 none O=C(Nc1ccc(OCC(F)(F)F)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 6, 8, 28, 31, 31, 31, 31, 8, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 8, 31, 31, 8, 8, 7, 7, 7, 7] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487615 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487615/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487615 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 341) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/341 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/341' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(OCC(F)(F)F)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487615.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487615/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001184487615 none O=C(Nc1ccc(OCC(F)(F)F)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 6, 8, 28, 31, 31, 31, 31, 8, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 8, 31, 31, 8, 8, 7, 7, 7, 7] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487615 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184487615 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487615/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487615/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487615 Building ZINC001184487615 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487615' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487615 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487615 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487615/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487615 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 340) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/340: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(OCC(F)(F)F)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487615.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487615/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001184487615 none O=C(Nc1ccc(OCC(F)(F)F)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 6, 8, 28, 31, 31, 31, 31, 8, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 8, 31, 31, 8, 8, 7, 7, 7, 7] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487615 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487615/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487615 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 341) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/341: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(OCC(F)(F)F)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487615.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487615/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001184487615 none O=C(Nc1ccc(OCC(F)(F)F)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 6, 8, 28, 31, 31, 31, 31, 8, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 8, 31, 31, 8, 8, 7, 7, 7, 7] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487615 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184487615 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487615/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487615/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487615 Building ZINC001184487381 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487381' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487381 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487381 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487381/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487381 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 342) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/342 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/342' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](c1ccccc1)C(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487381.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487381/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001184487381 none O=C(N[C@@H](c1ccccc1)C(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 11, 11, 14, 14, 11, 14, 14, 11, 11, 11, 11, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 14, 14, 11, 14, 14, 9, 9, 9, 9] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 67 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487381 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487381/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487381 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 343) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/343 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/343' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](c1ccccc1)C(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487381.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487381/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001184487381 none O=C(N[C@@H](c1ccccc1)C(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 11, 11, 17, 17, 17, 17, 17, 11, 11, 11, 11, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 17, 17, 17, 17, 17, 9, 9, 9, 9] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 64 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487381 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184487381 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487381/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487381/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487381 Building ZINC001184487381 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487381' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487381 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487381 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487381/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487381 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 342) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/342: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](c1ccccc1)C(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487381.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487381/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001184487381 none O=C(N[C@@H](c1ccccc1)C(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 11, 11, 14, 14, 11, 14, 14, 11, 11, 11, 11, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 14, 14, 11, 14, 14, 9, 9, 9, 9] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 67 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487381 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487381/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487381 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 343) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/343: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](c1ccccc1)C(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487381.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487381/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001184487381 none O=C(N[C@@H](c1ccccc1)C(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 11, 11, 17, 17, 17, 17, 17, 11, 11, 11, 11, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 17, 17, 17, 17, 17, 9, 9, 9, 9] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 64 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487381 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184487381 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487381/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487381/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487381 Building ZINC001184487718 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487718' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487718 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487718 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487718/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487718 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 344) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/344 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/344' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Cc2ccncc2)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487718.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487718/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001184487718 none O=C(Nc1ccc(Cc2ccncc2)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 1, 1, 1, 8, 1, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 7, 7, 6, 7, 26, 27, 27, 27, 27, 27, 7, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 7, 7, 26, 26, 27, 27, 27, 27, 7, 7, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487718 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487718/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487718 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 345) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/345 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/345' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Cc2ccncc2)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487718.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487718/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001184487718 none O=C(Nc1ccc(Cc2ccncc2)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 1, 1, 1, 8, 1, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 7, 7, 3, 3, 27, 28, 28, 27, 28, 28, 7, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 7, 7, 27, 27, 28, 28, 28, 28, 7, 7, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487718 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184487718 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487718/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487718/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487718 Building ZINC001184487718 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487718' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487718 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487718 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487718/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487718 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 344) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/344: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Cc2ccncc2)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487718.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487718/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001184487718 none O=C(Nc1ccc(Cc2ccncc2)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 1, 1, 1, 8, 1, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 7, 7, 6, 7, 26, 27, 27, 27, 27, 27, 7, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 7, 7, 26, 26, 27, 27, 27, 27, 7, 7, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487718 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487718/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487718 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 345) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/345: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Cc2ccncc2)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487718.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487718/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001184487718 none O=C(Nc1ccc(Cc2ccncc2)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 1, 1, 1, 8, 1, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 7, 7, 3, 3, 27, 28, 28, 27, 28, 28, 7, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 7, 7, 27, 27, 28, 28, 28, 28, 7, 7, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487718 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184487718 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487718/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487718/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487718 Building ZINC001184487819 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487819' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487819 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487819 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487819/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487819 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 346) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/346 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/346' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cc(C)nn3c3ccc(C(F)(F)F)cc3)c2c1) `ZINC001184487819.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184487819 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cc(C)nn3c3ccc(C(F)(F)F)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 5, 5, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 8, 8, 8, 8, 8, 8, 8, 8, 11, 20, 20, 20, 20, 20, 20, 20, 20, 8] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 52 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487819 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487819/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487819 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 347) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/347 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/347' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cc(C)nn3c3ccc(C(F)(F)F)cc3)c2c1) `ZINC001184487819.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487819/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184487819 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cc(C)nn3c3ccc(C(F)(F)F)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 5, 5, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 8, 8, 8, 8, 8, 8, 8, 8, 11, 20, 20, 20, 20, 20, 20, 20, 20, 8] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 52 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487819 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184487819 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487819/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487819/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487819 Building ZINC001184487819 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487819' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487819 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487819 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487819/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487819 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 346) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/346: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cc(C)nn3c3ccc(C(F)(F)F)cc3)c2c1) `ZINC001184487819.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184487819 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cc(C)nn3c3ccc(C(F)(F)F)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 5, 5, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 8, 8, 8, 8, 8, 8, 8, 8, 11, 20, 20, 20, 20, 20, 20, 20, 20, 8] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 52 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487819 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487819/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487819 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 347) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/347: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cc(C)nn3c3ccc(C(F)(F)F)cc3)c2c1) `ZINC001184487819.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487819/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184487819 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cc(C)nn3c3ccc(C(F)(F)F)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 5, 5, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 8, 8, 8, 8, 8, 8, 8, 8, 11, 20, 20, 20, 20, 20, 20, 20, 20, 8] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 52 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487819 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184487819 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487819/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487819/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487819 Building ZINC001184487812 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487812' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487812 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487812 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487812/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487812 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 348) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/348 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/348' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCc1nc2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2o1) `ZINC001184487812.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487812/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001184487812 none CCCc1nc2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 12, 12, 12, 12, 12, 12, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 35, 35, 35, 35, 35, 35, 35, 12, 12, 3, 4, 4, 4, 4, 12] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487812 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487812/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487812 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 349) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/349 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/349' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCc1nc2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2o1) `ZINC001184487812.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487812/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001184487812 none CCCc1nc2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 12, 12, 12, 12, 12, 12, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 35, 35, 35, 35, 35, 35, 35, 12, 12, 3, 4, 4, 4, 4, 12] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487812 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184487812 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487812/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487812/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487812 Building ZINC001184487812 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487812' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487812 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487812 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487812/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487812 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 348) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/348: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCc1nc2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2o1) `ZINC001184487812.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487812/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001184487812 none CCCc1nc2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 12, 12, 12, 12, 12, 12, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 35, 35, 35, 35, 35, 35, 35, 12, 12, 3, 4, 4, 4, 4, 12] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487812 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487812/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487812 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 349) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/349: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCc1nc2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2o1) `ZINC001184487812.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487812/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001184487812 none CCCc1nc2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 12, 12, 12, 12, 12, 12, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 35, 35, 35, 35, 35, 35, 35, 12, 12, 3, 4, 4, 4, 4, 12] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487812 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001184487812 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487812/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487812/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001184487812 Building ZINC001273898871 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273898871' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273898871 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001273898871 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273898871/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273898871 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 350) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/350 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/350' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](Sc2cccc(Cl)c2)C1) `ZINC001273898871.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001273898871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273898871/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001273898871 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](Sc2cccc(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 14, 1, 1, 1, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 6, 6, 2, 6, 6, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 9, 30, 30, 19, 30, 30, 30, 2, 2, 2, 2, 6, 6, 3, 6, 6, 2, 2, 2, 2, 2, 2, 2, 30, 30, 30, 30, 2, 2] 50 rigid atoms, others: [16, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 109 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273898871 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273898871/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273898871 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 351) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/351 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/351' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](Sc2cccc(Cl)c2)C1) `ZINC001273898871.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001273898871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273898871/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001273898871 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](Sc2cccc(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 14, 1, 1, 1, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 7, 7, 4, 7, 7, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 9, 31, 31, 16, 31, 31, 31, 2, 2, 2, 2, 7, 7, 7, 7, 7, 2, 2, 2, 2, 2, 2, 2, 31, 31, 31, 31, 2, 2] 50 rigid atoms, others: [16, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 123 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273898871 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001273898871 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273898871/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273898871/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273898871 Building ZINC001273898871 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273898871' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273898871 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001273898871 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273898871/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273898871 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 350) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/350: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](Sc2cccc(Cl)c2)C1) `ZINC001273898871.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001273898871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273898871/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001273898871 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](Sc2cccc(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 14, 1, 1, 1, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 6, 6, 2, 6, 6, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 9, 30, 30, 19, 30, 30, 30, 2, 2, 2, 2, 6, 6, 3, 6, 6, 2, 2, 2, 2, 2, 2, 2, 30, 30, 30, 30, 2, 2] 50 rigid atoms, others: [16, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 109 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273898871 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273898871/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273898871 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 351) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/351: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](Sc2cccc(Cl)c2)C1) `ZINC001273898871.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001273898871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273898871/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001273898871 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](Sc2cccc(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 14, 1, 1, 1, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 7, 7, 4, 7, 7, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 9, 31, 31, 16, 31, 31, 31, 2, 2, 2, 2, 7, 7, 7, 7, 7, 2, 2, 2, 2, 2, 2, 2, 31, 31, 31, 31, 2, 2] 50 rigid atoms, others: [16, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 123 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273898871 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001273898871 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273898871/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273898871/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273898871 Building ZINC001273898872 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273898872' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273898872 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001273898872 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273898872/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273898872 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 352) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/352 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/352' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](Sc2cccc(Cl)c2)C1) `ZINC001273898872.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001273898872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273898872/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001273898872 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](Sc2cccc(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 14, 1, 1, 1, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 6, 6, 2, 6, 6, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 10, 34, 34, 18, 34, 34, 34, 2, 2, 2, 2, 6, 6, 2, 6, 6, 2, 2, 2, 2, 2, 2, 2, 34, 34, 34, 34, 2, 2] 50 rigid atoms, others: [16, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 123 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273898872 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273898872/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273898872 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 353) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/353 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/353' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](Sc2cccc(Cl)c2)C1) `ZINC001273898872.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001273898872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273898872/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001273898872 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](Sc2cccc(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 14, 1, 1, 1, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 7, 7, 2, 7, 7, 2, 2, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 12, 33, 33, 24, 33, 33, 33, 3, 2, 2, 2, 7, 7, 2, 7, 7, 2, 2, 2, 3, 3, 3, 3, 33, 33, 33, 33, 3, 3] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 108 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273898872 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001273898872 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273898872/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273898872/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273898872 Building ZINC001273898872 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273898872' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273898872 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001273898872 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273898872/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273898872 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 352) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/352: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](Sc2cccc(Cl)c2)C1) `ZINC001273898872.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001273898872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273898872/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001273898872 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](Sc2cccc(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 14, 1, 1, 1, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 6, 6, 2, 6, 6, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 10, 34, 34, 18, 34, 34, 34, 2, 2, 2, 2, 6, 6, 2, 6, 6, 2, 2, 2, 2, 2, 2, 2, 34, 34, 34, 34, 2, 2] 50 rigid atoms, others: [16, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 123 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273898872 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273898872/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273898872 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 353) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/353: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](Sc2cccc(Cl)c2)C1) `ZINC001273898872.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001273898872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273898872/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001273898872 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](Sc2cccc(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 14, 1, 1, 1, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 7, 7, 2, 7, 7, 2, 2, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 12, 33, 33, 24, 33, 33, 33, 3, 2, 2, 2, 7, 7, 2, 7, 7, 2, 2, 2, 3, 3, 3, 3, 33, 33, 33, 33, 3, 3] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 108 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273898872 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001273898872 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273898872/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273898872/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273898872 Building ZINC001626138248 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001626138248' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001626138248 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626138248 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001626138248/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001626138248 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 354) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/354 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/354' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2scc(c3ccc(Cl)cc3)c2C(N)=O)cc1Cl) `ZINC001626138248.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626138248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001626138248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001626138248 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2scc(c3ccc(Cl)cc3)c2C(N)=O)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 8, 11, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 2, 6, 6, 1, 1, 1, 1, 2, 2, 2, 12, 12, 12, 12, 17, 17, 17, 17, 17, 17, 12, 12, 16, 16, 6, 6, 6, 11, 11, 11, 6, 6, 2, 12, 17, 17, 17, 17, 16, 16, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 73 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001626138248 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001626138248/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001626138248 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 355) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/355 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/355' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2scc(c3ccc(Cl)cc3)c2C(N)=O)cc1Cl) `ZINC001626138248.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626138248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001626138248/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001626138248 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2scc(c3ccc(Cl)cc3)c2C(N)=O)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 8, 11, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 2, 6, 6, 1, 1, 1, 1, 2, 2, 2, 12, 12, 12, 12, 17, 17, 12, 17, 17, 17, 12, 12, 16, 16, 6, 6, 6, 11, 11, 11, 6, 6, 2, 12, 17, 17, 17, 17, 16, 16, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 98 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001626138248 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001626138248 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001626138248/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001626138248/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001626138248 Building ZINC001626138248 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001626138248' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001626138248 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626138248 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001626138248/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001626138248 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 354) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/354: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2scc(c3ccc(Cl)cc3)c2C(N)=O)cc1Cl) `ZINC001626138248.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626138248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001626138248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001626138248 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2scc(c3ccc(Cl)cc3)c2C(N)=O)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 8, 11, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 2, 6, 6, 1, 1, 1, 1, 2, 2, 2, 12, 12, 12, 12, 17, 17, 17, 17, 17, 17, 12, 12, 16, 16, 6, 6, 6, 11, 11, 11, 6, 6, 2, 12, 17, 17, 17, 17, 16, 16, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 73 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001626138248 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001626138248/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001626138248 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 355) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/355: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2scc(c3ccc(Cl)cc3)c2C(N)=O)cc1Cl) `ZINC001626138248.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626138248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001626138248/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001626138248 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2scc(c3ccc(Cl)cc3)c2C(N)=O)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 8, 11, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 2, 6, 6, 1, 1, 1, 1, 2, 2, 2, 12, 12, 12, 12, 17, 17, 12, 17, 17, 17, 12, 12, 16, 16, 6, 6, 6, 11, 11, 11, 6, 6, 2, 12, 17, 17, 17, 17, 16, 16, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 98 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001626138248 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001626138248 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001626138248/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001626138248/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001626138248 Building ZINC001273994132 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273994132' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273994132 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001273994132 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273994132/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273994132 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 356) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/356 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/356' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)c1ccsc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001273994132.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001273994132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273994132/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001273994132 none CC(=O)c1ccsc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 10, 5, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 10, 10, 10, 5, 5, 2, 3, 3, 3, 13, 13, 3, 13, 3, 3, 3] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273994132 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273994132/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273994132 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 357) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/357 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/357' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)c1ccsc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001273994132.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001273994132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273994132/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001273994132 none CC(=O)c1ccsc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 12, 5, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 12, 12, 12, 5, 5, 2, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273994132 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001273994132 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273994132/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273994132/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273994132 Building ZINC001273994132 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273994132' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273994132 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001273994132 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273994132/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273994132 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 356) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/356: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)c1ccsc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001273994132.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001273994132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273994132/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001273994132 none CC(=O)c1ccsc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 10, 5, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 10, 10, 10, 5, 5, 2, 3, 3, 3, 13, 13, 3, 13, 3, 3, 3] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273994132 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273994132/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273994132 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 357) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/357: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)c1ccsc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001273994132.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001273994132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273994132/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001273994132 none CC(=O)c1ccsc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 12, 5, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 12, 12, 12, 5, 5, 2, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273994132 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001273994132 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273994132/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273994132/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001273994132 Building ZINC001274144192 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001274144192 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 358) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/358 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/358' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001274144192.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001274144192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001274144192 none CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 5, 5, 5, 5, 5, 5, 18, 25, 25, 18, 22, 25, 25, 5, 5, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 5, 18, 18, 25, 25, 25, 25, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 129 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 359) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/359 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/359' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001274144192.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001274144192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001274144192 none CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 5, 5, 5, 5, 5, 5, 18, 25, 25, 18, 22, 25, 25, 5, 5, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 5, 18, 18, 25, 25, 25, 25, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 129 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 360) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/360 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/360' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001274144192.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001274144192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001274144192 none CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 4, 4, 4, 4, 4, 4, 16, 24, 24, 16, 16, 24, 24, 4, 4, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 16, 16, 24, 24, 24, 24, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 118 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 361) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/361 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/361' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001274144192.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001274144192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001274144192 none CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 4, 4, 4, 4, 4, 4, 16, 24, 24, 16, 16, 24, 24, 4, 4, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 16, 16, 24, 24, 24, 24, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 118 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001274144192 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192 Building ZINC001274144192 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001274144192 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 358) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/358: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001274144192.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001274144192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001274144192 none CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 5, 5, 5, 5, 5, 5, 18, 25, 25, 18, 22, 25, 25, 5, 5, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 5, 18, 18, 25, 25, 25, 25, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 129 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 359) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/359: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001274144192.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001274144192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001274144192 none CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 5, 5, 5, 5, 5, 5, 18, 25, 25, 18, 22, 25, 25, 5, 5, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 5, 18, 18, 25, 25, 25, 25, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 129 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 360) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/360: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001274144192.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001274144192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001274144192 none CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 4, 4, 4, 4, 4, 4, 16, 24, 24, 16, 16, 24, 24, 4, 4, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 16, 16, 24, 24, 24, 24, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 118 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 361) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/361: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001274144192.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001274144192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001274144192 none CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 4, 4, 4, 4, 4, 4, 16, 24, 24, 16, 16, 24, 24, 4, 4, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 16, 16, 24, 24, 24, 24, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 118 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001274144192 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192 Building ZINC001274144192 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001274144192 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 358) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/358: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001274144192.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001274144192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001274144192 none CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 5, 5, 5, 5, 5, 5, 18, 25, 25, 18, 22, 25, 25, 5, 5, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 5, 18, 18, 25, 25, 25, 25, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 129 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 359) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/359: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001274144192.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001274144192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001274144192 none CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 5, 5, 5, 5, 5, 5, 18, 25, 25, 18, 22, 25, 25, 5, 5, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 5, 18, 18, 25, 25, 25, 25, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 129 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 360) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/360: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001274144192.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001274144192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001274144192 none CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 4, 4, 4, 4, 4, 4, 16, 24, 24, 16, 16, 24, 24, 4, 4, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 16, 16, 24, 24, 24, 24, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 118 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 361) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/361: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001274144192.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001274144192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001274144192 none CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 4, 4, 4, 4, 4, 4, 16, 24, 24, 16, 16, 24, 24, 4, 4, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 16, 16, 24, 24, 24, 24, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 118 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001274144192 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192 Building ZINC001274144192 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001274144192 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 358) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/358: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001274144192.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001274144192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001274144192 none CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 5, 5, 5, 5, 5, 5, 18, 25, 25, 18, 22, 25, 25, 5, 5, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 5, 18, 18, 25, 25, 25, 25, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 129 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 359) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/359: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001274144192.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001274144192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001274144192 none CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 5, 5, 5, 5, 5, 5, 18, 25, 25, 18, 22, 25, 25, 5, 5, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 5, 18, 18, 25, 25, 25, 25, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 129 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 360) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/360: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001274144192.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001274144192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001274144192 none CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 4, 4, 4, 4, 4, 4, 16, 24, 24, 16, 16, 24, 24, 4, 4, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 16, 16, 24, 24, 24, 24, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 118 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 361) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/361: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001274144192.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001274144192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001274144192 none CC(C)C[C@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 4, 4, 4, 4, 4, 4, 16, 24, 24, 16, 16, 24, 24, 4, 4, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 16, 16, 24, 24, 24, 24, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 118 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001274144192 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144192 Building ZINC001274144193 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001274144193 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 362) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/362 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/362' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001274144193.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001274144193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001274144193 none CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 28, 28, 21, 24, 28, 28, 6, 6, 6, 2, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 28, 28, 28, 28, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 117 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 363) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/363 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/363' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001274144193.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001274144193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001274144193 none CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 28, 28, 21, 24, 28, 28, 6, 6, 6, 2, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 28, 28, 28, 28, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 117 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 364) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/364 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/364' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001274144193.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001274144193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001274144193 none CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 7, 7, 7, 7, 7, 7, 21, 26, 26, 21, 23, 26, 26, 7, 7, 7, 2, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 7, 7, 21, 21, 26, 26, 26, 26, 7, 7, 7, 7, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 119 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 365) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/365 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/365' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001274144193.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001274144193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001274144193 none CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 7, 7, 7, 7, 7, 7, 21, 26, 26, 21, 23, 26, 26, 7, 7, 7, 2, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 7, 7, 21, 21, 26, 26, 26, 26, 7, 7, 7, 7, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 119 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001274144193 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193 Building ZINC001274144193 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001274144193 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 362) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/362: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001274144193.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001274144193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001274144193 none CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 28, 28, 21, 24, 28, 28, 6, 6, 6, 2, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 28, 28, 28, 28, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 117 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 363) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/363: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001274144193.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001274144193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001274144193 none CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 28, 28, 21, 24, 28, 28, 6, 6, 6, 2, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 28, 28, 28, 28, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 117 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 364) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/364: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001274144193.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001274144193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001274144193 none CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 7, 7, 7, 7, 7, 7, 21, 26, 26, 21, 23, 26, 26, 7, 7, 7, 2, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 7, 7, 21, 21, 26, 26, 26, 26, 7, 7, 7, 7, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 119 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 365) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/365: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001274144193.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001274144193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001274144193 none CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 7, 7, 7, 7, 7, 7, 21, 26, 26, 21, 23, 26, 26, 7, 7, 7, 2, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 7, 7, 21, 21, 26, 26, 26, 26, 7, 7, 7, 7, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 119 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001274144193 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193 Building ZINC001274144193 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001274144193 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 362) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/362: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001274144193.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001274144193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001274144193 none CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 28, 28, 21, 24, 28, 28, 6, 6, 6, 2, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 28, 28, 28, 28, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 117 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 363) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/363: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001274144193.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001274144193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001274144193 none CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 28, 28, 21, 24, 28, 28, 6, 6, 6, 2, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 28, 28, 28, 28, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 117 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 364) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/364: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001274144193.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001274144193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001274144193 none CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 7, 7, 7, 7, 7, 7, 21, 26, 26, 21, 23, 26, 26, 7, 7, 7, 2, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 7, 7, 21, 21, 26, 26, 26, 26, 7, 7, 7, 7, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 119 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 365) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/365: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001274144193.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001274144193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001274144193 none CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 7, 7, 7, 7, 7, 7, 21, 26, 26, 21, 23, 26, 26, 7, 7, 7, 2, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 7, 7, 21, 21, 26, 26, 26, 26, 7, 7, 7, 7, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 119 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001274144193 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193 Building ZINC001274144193 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001274144193 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 362) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/362: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001274144193.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001274144193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001274144193 none CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 28, 28, 21, 24, 28, 28, 6, 6, 6, 2, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 28, 28, 28, 28, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 117 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 363) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/363: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001274144193.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001274144193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001274144193 none CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 28, 28, 21, 24, 28, 28, 6, 6, 6, 2, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 28, 28, 28, 28, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 117 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 364) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/364: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001274144193.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001274144193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001274144193 none CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 7, 7, 7, 7, 7, 7, 21, 26, 26, 21, 23, 26, 26, 7, 7, 7, 2, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 7, 7, 21, 21, 26, 26, 26, 26, 7, 7, 7, 7, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 119 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 365) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/365: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001274144193.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001274144193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001274144193 none CC(C)C[C@@H]1CN(Cc2ccc(Cl)cc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 7, 7, 7, 7, 7, 7, 21, 26, 26, 21, 23, 26, 26, 7, 7, 7, 2, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 7, 7, 21, 21, 26, 26, 26, 26, 7, 7, 7, 7, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 119 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001274144193 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274144193 Building ZINC001274515318 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274515318' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274515318 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001274515318 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274515318/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274515318 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 366) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/366 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/366' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ncc(c2ccc(Br)cc2)s1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001274515318.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001274515318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274515318/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001274515318 none O=C(Nc1ncc(c2ccc(Br)cc2)s1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 14, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 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, 1, 6, 6, 10, 10, 10, 10, 38, 38, 14, 17, 38, 38, 10, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 6, 10, 38, 38, 38, 38, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274515318 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274515318/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274515318 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 367) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/367 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/367' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ncc(c2ccc(Br)cc2)s1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001274515318.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001274515318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274515318/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001274515318 none O=C(Nc1ncc(c2ccc(Br)cc2)s1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 14, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 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, 1, 6, 6, 10, 10, 10, 10, 34, 34, 18, 19, 34, 34, 10, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 6, 10, 34, 34, 34, 34, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274515318 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001274515318 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274515318/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274515318/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274515318 Building ZINC001274515318 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274515318' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274515318 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001274515318 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274515318/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274515318 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 366) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/366: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ncc(c2ccc(Br)cc2)s1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001274515318.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001274515318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274515318/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001274515318 none O=C(Nc1ncc(c2ccc(Br)cc2)s1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 14, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 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, 1, 6, 6, 10, 10, 10, 10, 38, 38, 14, 17, 38, 38, 10, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 6, 10, 38, 38, 38, 38, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274515318 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274515318/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274515318 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 367) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/367: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ncc(c2ccc(Br)cc2)s1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001274515318.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001274515318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274515318/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001274515318 none O=C(Nc1ncc(c2ccc(Br)cc2)s1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 14, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 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, 1, 6, 6, 10, 10, 10, 10, 34, 34, 18, 19, 34, 34, 10, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 6, 10, 34, 34, 34, 34, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274515318 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001274515318 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274515318/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274515318/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274515318 Building ZINC001274546217 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274546217' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274546217 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001274546217 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274546217/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274546217 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 368) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/368 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/368' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC(C)(C)Cc2ccc(Br)c(C)c2)cc1Cl) `ZINC001274546217.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001274546217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274546217/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001274546217 none COc1ccc([C@]([O-])([SiH3])C(=O)NC(C)(C)Cc2ccc(Br)c(C)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 17, 1, 5, 1, 1, 1, 16, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 14, 25, 25, 15, 25, 25, 25, 25, 4, 4, 4, 8, 8, 8, 4, 4, 2, 5, 5, 5, 5, 5, 5, 14, 14, 25, 25, 25, 25, 25, 25, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274546217 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274546217/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274546217 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 369) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/369 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/369' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC(C)(C)Cc2ccc(Br)c(C)c2)cc1Cl) `ZINC001274546217.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001274546217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274546217/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001274546217 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC(C)(C)Cc2ccc(Br)c(C)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 17, 1, 5, 1, 1, 1, 16, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 15, 26, 26, 17, 26, 26, 26, 26, 4, 4, 4, 8, 8, 8, 4, 4, 3, 6, 6, 6, 6, 6, 6, 15, 15, 26, 26, 26, 26, 26, 26, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274546217 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001274546217 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274546217/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274546217/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274546217 Building ZINC001274546217 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274546217' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274546217 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001274546217 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274546217/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274546217 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 368) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/368: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC(C)(C)Cc2ccc(Br)c(C)c2)cc1Cl) `ZINC001274546217.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001274546217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274546217/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001274546217 none COc1ccc([C@]([O-])([SiH3])C(=O)NC(C)(C)Cc2ccc(Br)c(C)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 17, 1, 5, 1, 1, 1, 16, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 14, 25, 25, 15, 25, 25, 25, 25, 4, 4, 4, 8, 8, 8, 4, 4, 2, 5, 5, 5, 5, 5, 5, 14, 14, 25, 25, 25, 25, 25, 25, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274546217 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274546217/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274546217 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 369) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/369: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC(C)(C)Cc2ccc(Br)c(C)c2)cc1Cl) `ZINC001274546217.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001274546217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274546217/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001274546217 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC(C)(C)Cc2ccc(Br)c(C)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 17, 1, 5, 1, 1, 1, 16, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 15, 26, 26, 17, 26, 26, 26, 26, 4, 4, 4, 8, 8, 8, 4, 4, 3, 6, 6, 6, 6, 6, 6, 15, 15, 26, 26, 26, 26, 26, 26, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274546217 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001274546217 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274546217/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274546217/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274546217 Building ZINC001274555261 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555261' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555261 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001274555261 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555261/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555261 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 370) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/370 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/370' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(C)(C2CC2)CC1) `ZINC001274555261.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001274555261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555261/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001274555261 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(C)(C2CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 1, 1, 1, 2, 4, 4, 7, 7, 7, 7, 7, 9, 9, 7, 7, 2, 2, 2, 17, 17, 17, 17, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 9, 9, 9, 9, 9, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 44 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555261 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555261/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555261 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 371) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/371 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/371' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(C)(C2CC2)CC1) `ZINC001274555261.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001274555261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555261/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001274555261 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(C)(C2CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 14, 14, 6, 14, 14, 14, 14, 14, 14, 2, 2, 1, 1, 1, 2, 4, 4, 7, 7, 7, 7, 7, 13, 13, 7, 7, 2, 2, 2, 14, 14, 7, 14, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 13, 13, 13, 13, 13, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 67 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555261 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001274555261 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555261/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555261/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555261 Building ZINC001274555261 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555261' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555261 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001274555261 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555261/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555261 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 370) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/370: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(C)(C2CC2)CC1) `ZINC001274555261.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001274555261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555261/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001274555261 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(C)(C2CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 1, 1, 1, 2, 4, 4, 7, 7, 7, 7, 7, 9, 9, 7, 7, 2, 2, 2, 17, 17, 17, 17, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 9, 9, 9, 9, 9, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 44 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555261 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555261/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555261 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 371) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/371: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(C)(C2CC2)CC1) `ZINC001274555261.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001274555261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555261/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001274555261 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(C)(C2CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 14, 14, 6, 14, 14, 14, 14, 14, 14, 2, 2, 1, 1, 1, 2, 4, 4, 7, 7, 7, 7, 7, 13, 13, 7, 7, 2, 2, 2, 14, 14, 7, 14, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 13, 13, 13, 13, 13, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 67 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555261 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001274555261 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555261/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555261/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555261 Building ZINC001274555921 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555921' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555921 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001274555921 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555921/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555921 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 372) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/372 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/372' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC(C)(C)Oc3ccc(NC(=O)OC(C)(C)C)cc32)c1) `ZINC001274555921.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001274555921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555921/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001274555921 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC(C)(C)Oc3ccc(NC(=O)OC(C)(C)C)cc32)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 7, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 18, 25, 25, 28, 28, 28, 28, 5, 5, 4, 4, 4, 4, 2, 4, 4, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 18, 28, 28, 28, 28, 28, 28, 28, 28, 28, 5, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555921 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555921/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555921 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 373) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/373 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/373' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)N[C@H]2CC(C)(C)Oc3ccc(NC(=O)OC(C)(C)C)cc32)c1) `ZINC001274555921.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001274555921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555921/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001274555921 none Cc1cccc([C@]([O-])([SiH3])C(=O)N[C@H]2CC(C)(C)Oc3ccc(NC(=O)OC(C)(C)C)cc32)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 7, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 18, 25, 25, 26, 26, 26, 26, 5, 5, 4, 4, 4, 4, 2, 4, 4, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 18, 26, 26, 26, 26, 26, 26, 26, 26, 26, 5, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555921 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001274555921 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555921/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555921/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555921 Building ZINC001274555921 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555921' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555921 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001274555921 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555921/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555921 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 372) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/372: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC(C)(C)Oc3ccc(NC(=O)OC(C)(C)C)cc32)c1) `ZINC001274555921.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001274555921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555921/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001274555921 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC(C)(C)Oc3ccc(NC(=O)OC(C)(C)C)cc32)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 7, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 18, 25, 25, 28, 28, 28, 28, 5, 5, 4, 4, 4, 4, 2, 4, 4, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 18, 28, 28, 28, 28, 28, 28, 28, 28, 28, 5, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555921 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555921/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555921 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 373) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/373: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)N[C@H]2CC(C)(C)Oc3ccc(NC(=O)OC(C)(C)C)cc32)c1) `ZINC001274555921.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001274555921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555921/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001274555921 none Cc1cccc([C@]([O-])([SiH3])C(=O)N[C@H]2CC(C)(C)Oc3ccc(NC(=O)OC(C)(C)C)cc32)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 7, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 18, 25, 25, 26, 26, 26, 26, 5, 5, 4, 4, 4, 4, 2, 4, 4, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 18, 26, 26, 26, 26, 26, 26, 26, 26, 26, 5, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555921 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001274555921 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555921/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555921/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555921 Building ZINC001274555922 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555922' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555922 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001274555922 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555922/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555922 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 374) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/374 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/374' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CC(C)(C)Oc3ccc(NC(=O)OC(C)(C)C)cc32)c1) `ZINC001274555922.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001274555922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555922/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001274555922 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CC(C)(C)Oc3ccc(NC(=O)OC(C)(C)C)cc32)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 7, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 18, 25, 25, 27, 27, 27, 27, 5, 5, 4, 4, 4, 4, 2, 4, 4, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 18, 27, 27, 27, 27, 27, 27, 27, 27, 27, 5, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555922 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555922/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555922 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 375) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/375 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/375' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CC(C)(C)Oc3ccc(NC(=O)OC(C)(C)C)cc32)c1) `ZINC001274555922.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001274555922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555922/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001274555922 none Cc1cccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CC(C)(C)Oc3ccc(NC(=O)OC(C)(C)C)cc32)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 7, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 4, 4, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 19, 26, 26, 29, 29, 29, 29, 5, 5, 4, 4, 4, 4, 1, 4, 4, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 19, 29, 29, 29, 29, 29, 29, 29, 29, 29, 5, 4] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555922 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001274555922 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555922/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555922/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555922 Building ZINC001274555922 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555922' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555922 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001274555922 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555922/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555922 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 374) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/374: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CC(C)(C)Oc3ccc(NC(=O)OC(C)(C)C)cc32)c1) `ZINC001274555922.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001274555922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555922/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001274555922 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CC(C)(C)Oc3ccc(NC(=O)OC(C)(C)C)cc32)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 7, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 18, 25, 25, 27, 27, 27, 27, 5, 5, 4, 4, 4, 4, 2, 4, 4, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 18, 27, 27, 27, 27, 27, 27, 27, 27, 27, 5, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555922 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555922/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555922 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 375) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/375: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CC(C)(C)Oc3ccc(NC(=O)OC(C)(C)C)cc32)c1) `ZINC001274555922.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001274555922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555922/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001274555922 none Cc1cccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CC(C)(C)Oc3ccc(NC(=O)OC(C)(C)C)cc32)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 7, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 4, 4, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 19, 26, 26, 29, 29, 29, 29, 5, 5, 4, 4, 4, 4, 1, 4, 4, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 19, 29, 29, 29, 29, 29, 29, 29, 29, 29, 5, 4] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555922 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001274555922 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555922/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555922/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001274555922 Building ZINC000466796972 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466796972' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466796972 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000466796972 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466796972/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466796972 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 376) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/376 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/376' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2ccccc2[C@]1(C)C(F)(F)F) `ZINC000466796972.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000466796972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466796972/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000466796972 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2ccccc2[C@]1(C)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 13, 13, 7, 13, 13, 4, 4, 1, 1, 1, 1, 4, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 4, 4, 4, 13, 13, 8, 13, 13, 4, 4, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 28 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 54 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466796972 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466796972/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466796972 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 377) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/377 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/377' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2ccccc2[C@]1(C)C(F)(F)F) `ZINC000466796972.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000466796972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466796972/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000466796972 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2ccccc2[C@]1(C)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 12, 12, 8, 12, 12, 4, 4, 1, 1, 1, 1, 4, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 4, 12, 12, 8, 12, 12, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 29 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 48 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466796972 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000466796972 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466796972/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466796972/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466796972 Building ZINC000466796972 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466796972' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466796972 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000466796972 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466796972/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466796972 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 376) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/376: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2ccccc2[C@]1(C)C(F)(F)F) `ZINC000466796972.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000466796972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466796972/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000466796972 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2ccccc2[C@]1(C)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 13, 13, 7, 13, 13, 4, 4, 1, 1, 1, 1, 4, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 4, 4, 4, 13, 13, 8, 13, 13, 4, 4, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 28 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 54 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466796972 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466796972/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466796972 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 377) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/377: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2ccccc2[C@]1(C)C(F)(F)F) `ZINC000466796972.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000466796972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466796972/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000466796972 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2ccccc2[C@]1(C)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 12, 12, 8, 12, 12, 4, 4, 1, 1, 1, 1, 4, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 4, 12, 12, 8, 12, 12, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 29 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 48 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466796972 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000466796972 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466796972/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466796972/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466796972 Building ZINC000466796973 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466796973' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466796973 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000466796973 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466796973/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466796973 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 378) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/378 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/378' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2ccccc2[C@@]1(C)C(F)(F)F) `ZINC000466796973.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000466796973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466796973/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000466796973 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2ccccc2[C@@]1(C)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 11, 11, 8, 11, 11, 4, 4, 1, 1, 1, 1, 4, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 4, 11, 11, 8, 11, 11, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 28 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 44 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466796973 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466796973/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466796973 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 379) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/379 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/379' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2ccccc2[C@@]1(C)C(F)(F)F) `ZINC000466796973.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000466796973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466796973/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000466796973 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2ccccc2[C@@]1(C)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 13, 13, 4, 13, 13, 4, 4, 1, 1, 1, 1, 4, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 4, 4, 4, 13, 13, 4, 13, 13, 4, 4, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 27 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 55 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466796973 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000466796973 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466796973/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466796973/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466796973 Building ZINC000466796973 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466796973' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466796973 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000466796973 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466796973/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466796973 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 378) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/378: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2ccccc2[C@@]1(C)C(F)(F)F) `ZINC000466796973.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000466796973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466796973/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000466796973 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2ccccc2[C@@]1(C)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 11, 11, 8, 11, 11, 4, 4, 1, 1, 1, 1, 4, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 4, 11, 11, 8, 11, 11, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 28 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 44 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466796973 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466796973/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466796973 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 379) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/379: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2ccccc2[C@@]1(C)C(F)(F)F) `ZINC000466796973.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000466796973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466796973/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000466796973 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2ccccc2[C@@]1(C)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 13, 13, 4, 13, 13, 4, 4, 1, 1, 1, 1, 4, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 4, 4, 4, 13, 13, 4, 13, 13, 4, 4, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 27 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 55 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466796973 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000466796973 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466796973/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466796973/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466796973 Building ZINC001275262215 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262215' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262215 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001275262215 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262215/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262215 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 380) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/380 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/380' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@H]([C@@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001275262215.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001275262215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262215/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC001275262215 none CC(C)(C)OC(=O)N1CCC[C@H]([C@@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 35, 17, 35, 17, 17, 17, 17, 7, 17, 7, 8, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 17, 17, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 3, 17, 17] 50 rigid atoms, others: [20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 140 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262215 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262215/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262215 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 381) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/381 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/381' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@H]([C@@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001275262215.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001275262215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262215/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC001275262215 none CC(C)(C)OC(=O)N1CCC[C@H]([C@@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 22, 37, 22, 22, 22, 22, 6, 22, 6, 8, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 22, 22, 22, 6, 6, 6, 6, 6, 6, 6, 6, 2, 2, 2, 2, 22, 22] 50 rigid atoms, others: [20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 139 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262215 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001275262215 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262215/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262215/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262215 Building ZINC001275262215 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262215' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262215 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001275262215 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262215/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262215 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 380) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/380: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@H]([C@@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001275262215.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001275262215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262215/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC001275262215 none CC(C)(C)OC(=O)N1CCC[C@H]([C@@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 35, 17, 35, 17, 17, 17, 17, 7, 17, 7, 8, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 17, 17, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 3, 17, 17] 50 rigid atoms, others: [20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 140 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262215 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262215/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262215 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 381) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/381: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@H]([C@@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001275262215.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001275262215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262215/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC001275262215 none CC(C)(C)OC(=O)N1CCC[C@H]([C@@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 22, 37, 22, 22, 22, 22, 6, 22, 6, 8, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 22, 22, 22, 6, 6, 6, 6, 6, 6, 6, 6, 2, 2, 2, 2, 22, 22] 50 rigid atoms, others: [20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 139 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262215 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001275262215 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262215/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262215/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262215 Building ZINC001275262216 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262216' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262216 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001275262216 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262216/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262216 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 382) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/382 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/382' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@@H]([C@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001275262216.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001275262216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262216/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC001275262216 none CC(C)(C)OC(=O)N1CCC[C@@H]([C@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 19, 33, 19, 19, 19, 19, 6, 19, 6, 8, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 19, 19, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 3, 3, 19, 19] 50 rigid atoms, others: [20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 143 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262216 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262216/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262216 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 383) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/383 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/383' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@@H]([C@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001275262216.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001275262216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262216/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC001275262216 none CC(C)(C)OC(=O)N1CCC[C@@H]([C@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 18, 34, 18, 18, 18, 18, 7, 18, 7, 8, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 18, 18, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 3, 18, 18] 50 rigid atoms, others: [20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 138 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262216 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001275262216 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262216/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262216/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262216 Building ZINC001275262216 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262216' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262216 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001275262216 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262216/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262216 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 382) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/382: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@@H]([C@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001275262216.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001275262216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262216/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC001275262216 none CC(C)(C)OC(=O)N1CCC[C@@H]([C@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 19, 33, 19, 19, 19, 19, 6, 19, 6, 8, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 19, 19, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 3, 3, 19, 19] 50 rigid atoms, others: [20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 143 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262216 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262216/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262216 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 383) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/383: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@@H]([C@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001275262216.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001275262216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262216/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC001275262216 none CC(C)(C)OC(=O)N1CCC[C@@H]([C@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 18, 34, 18, 18, 18, 18, 7, 18, 7, 8, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 18, 18, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 3, 18, 18] 50 rigid atoms, others: [20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 138 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262216 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001275262216 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262216/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262216/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262216 Building ZINC001275262217 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262217' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262217 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001275262217 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262217/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262217 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 384) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/384 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/384' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@@H]([C@@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001275262217.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001275262217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262217/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC001275262217 none CC(C)(C)OC(=O)N1CCC[C@@H]([C@@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 35, 18, 35, 18, 18, 18, 18, 6, 18, 6, 6, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 18, 18, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 3, 3, 18, 18] 50 rigid atoms, others: [20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262217 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262217/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262217 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 385) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/385 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/385' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@@H]([C@@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001275262217.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001275262217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262217/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC001275262217 none CC(C)(C)OC(=O)N1CCC[C@@H]([C@@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 21, 34, 21, 21, 21, 21, 7, 21, 7, 7, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 21, 21, 21, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 3, 21, 21] 50 rigid atoms, others: [20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262217 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001275262217 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262217/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262217/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262217 Building ZINC001275262217 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262217' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262217 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001275262217 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262217/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262217 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 384) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/384: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@@H]([C@@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001275262217.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001275262217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262217/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC001275262217 none CC(C)(C)OC(=O)N1CCC[C@@H]([C@@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 35, 18, 35, 18, 18, 18, 18, 6, 18, 6, 6, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 18, 18, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 3, 3, 18, 18] 50 rigid atoms, others: [20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262217 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262217/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262217 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 385) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/385: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@@H]([C@@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001275262217.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001275262217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262217/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC001275262217 none CC(C)(C)OC(=O)N1CCC[C@@H]([C@@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 21, 34, 21, 21, 21, 21, 7, 21, 7, 7, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 21, 21, 21, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 3, 21, 21] 50 rigid atoms, others: [20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262217 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001275262217 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262217/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262217/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262217 Building ZINC001275262218 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262218' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262218 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001275262218 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262218/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262218 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 386) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/386 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/386' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@H]([C@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001275262218.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001275262218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC001275262218 none CC(C)(C)OC(=O)N1CCC[C@H]([C@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 36, 24, 36, 24, 24, 24, 24, 7, 24, 7, 7, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24, 24, 24, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 3, 24, 24] 50 rigid atoms, others: [20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262218 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262218/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262218 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 387) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/387 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/387' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@H]([C@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001275262218.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001275262218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262218/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC001275262218 none CC(C)(C)OC(=O)N1CCC[C@H]([C@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 17, 33, 17, 17, 17, 17, 6, 17, 6, 6, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 17, 17, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 3, 3, 17, 17] 50 rigid atoms, others: [20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262218 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001275262218 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262218/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262218/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262218 Building ZINC001275262218 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262218' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262218 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001275262218 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262218/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262218 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 386) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/386: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@H]([C@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001275262218.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001275262218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC001275262218 none CC(C)(C)OC(=O)N1CCC[C@H]([C@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 36, 24, 36, 24, 24, 24, 24, 7, 24, 7, 7, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24, 24, 24, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 3, 24, 24] 50 rigid atoms, others: [20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262218 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262218/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262218 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 387) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/387: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@H]([C@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001275262218.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001275262218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262218/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC001275262218 none CC(C)(C)OC(=O)N1CCC[C@H]([C@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 17, 33, 17, 17, 17, 17, 6, 17, 6, 6, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 17, 17, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 3, 3, 17, 17] 50 rigid atoms, others: [20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262218 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001275262218 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262218/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262218/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275262218 Building ZINC001275343576 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275343576' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275343576 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001275343576 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275343576/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275343576 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 388) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/388 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/388' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCc3c(Cl)ccc(Br)c32)cc1Cl) `ZINC001275343576.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001275343576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275343576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001275343576 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCc3c(Cl)ccc(Br)c32)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 16, 1, 1, 1, 17, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [12, 8, 3, 8, 8, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 12, 12, 12, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 28 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275343576 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275343576/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275343576 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 389) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/389 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/389' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCc3c(Cl)ccc(Br)c32)cc1Cl) `ZINC001275343576.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001275343576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275343576/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001275343576 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCc3c(Cl)ccc(Br)c32)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 16, 1, 1, 1, 17, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [12, 8, 2, 8, 8, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 12, 12, 12, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 28 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275343576 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001275343576 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275343576/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275343576/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275343576 Building ZINC001275343576 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275343576' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275343576 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001275343576 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275343576/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275343576 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 388) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/388: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCc3c(Cl)ccc(Br)c32)cc1Cl) `ZINC001275343576.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001275343576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275343576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001275343576 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCc3c(Cl)ccc(Br)c32)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 16, 1, 1, 1, 17, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [12, 8, 3, 8, 8, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 12, 12, 12, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 28 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275343576 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275343576/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275343576 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 389) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/389: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCc3c(Cl)ccc(Br)c32)cc1Cl) `ZINC001275343576.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001275343576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275343576/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001275343576 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCc3c(Cl)ccc(Br)c32)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 16, 1, 1, 1, 17, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [12, 8, 2, 8, 8, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 12, 12, 12, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 28 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275343576 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001275343576 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275343576/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275343576/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275343576 Building ZINC001275353915 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275353915' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275353915 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001275353915 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275353915/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275353915 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 390) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/390 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/390' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]1c1ccccc1F) `ZINC001275353915.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001275353915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275353915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001275353915 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]1c1ccccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 15, 15, 5, 15, 15, 15, 15, 15, 15, 3, 3, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 14, 14, 12, 14, 14, 14, 3, 3, 3, 15, 15, 12, 15, 3, 3, 3, 3, 9, 9, 14, 14, 14, 14] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 93 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275353915 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275353915/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275353915 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 391) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/391 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/391' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]1c1ccccc1F) `ZINC001275353915.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001275353915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275353915/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001275353915 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]1c1ccccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 17, 17, 6, 17, 17, 17, 17, 17, 17, 3, 3, 1, 1, 1, 1, 2, 2, 2, 10, 10, 10, 10, 10, 11, 11, 10, 11, 11, 11, 3, 3, 3, 17, 17, 10, 17, 3, 3, 3, 2, 10, 10, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 83 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275353915 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001275353915 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275353915/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275353915/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275353915 Building ZINC001275353915 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275353915' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275353915 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001275353915 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275353915/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275353915 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 390) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/390: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]1c1ccccc1F) `ZINC001275353915.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001275353915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275353915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001275353915 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]1c1ccccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 15, 15, 5, 15, 15, 15, 15, 15, 15, 3, 3, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 14, 14, 12, 14, 14, 14, 3, 3, 3, 15, 15, 12, 15, 3, 3, 3, 3, 9, 9, 14, 14, 14, 14] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 93 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275353915 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275353915/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275353915 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 391) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/391: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]1c1ccccc1F) `ZINC001275353915.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001275353915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275353915/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001275353915 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]1c1ccccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 17, 17, 6, 17, 17, 17, 17, 17, 17, 3, 3, 1, 1, 1, 1, 2, 2, 2, 10, 10, 10, 10, 10, 11, 11, 10, 11, 11, 11, 3, 3, 3, 17, 17, 10, 17, 3, 3, 3, 2, 10, 10, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 83 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275353915 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001275353915 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275353915/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275353915/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275353915 Building ZINC000543782125 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543782125' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543782125 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000543782125 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543782125/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543782125 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 392) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/392 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/392' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CCN(Cc2ccsc2)C(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)cc1OC) `ZINC000543782125.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000543782125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543782125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000543782125 none COc1ccc(CCN(Cc2ccsc2)C(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 1, 14, 1, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 14, 7, 7, 4, 2, 4, 6, 12, 12, 12, 12, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 28, 26, 26, 26, 14, 14, 7, 7, 7, 7, 6, 6, 12, 12, 12, 1, 1, 1, 1, 1, 1, 14, 28, 28, 28] 50 rigid atoms, others: [50, 49, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 51, 52, 53, 54]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543782125 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543782125/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543782125 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 393) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/393 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/393' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CCN(Cc2ccsc2)C(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)cc1OC) `ZINC000543782125.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000543782125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543782125/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000543782125 none COc1ccc(CCN(Cc2ccsc2)C(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 1, 14, 1, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 12, 7, 7, 4, 2, 4, 6, 11, 11, 11, 11, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 26, 24, 24, 24, 12, 12, 7, 7, 7, 7, 6, 6, 11, 11, 11, 1, 1, 1, 1, 1, 1, 12, 26, 26, 26] 50 rigid atoms, others: [50, 49, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 51, 52, 53, 54]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543782125 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000543782125 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543782125/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543782125/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543782125 Building ZINC000543782125 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543782125' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543782125 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000543782125 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543782125/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543782125 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 392) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/392: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CCN(Cc2ccsc2)C(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)cc1OC) `ZINC000543782125.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000543782125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543782125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000543782125 none COc1ccc(CCN(Cc2ccsc2)C(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 1, 14, 1, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 14, 7, 7, 4, 2, 4, 6, 12, 12, 12, 12, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 28, 26, 26, 26, 14, 14, 7, 7, 7, 7, 6, 6, 12, 12, 12, 1, 1, 1, 1, 1, 1, 14, 28, 28, 28] 50 rigid atoms, others: [50, 49, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 51, 52, 53, 54]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543782125 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543782125/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543782125 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 393) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/393: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CCN(Cc2ccsc2)C(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)cc1OC) `ZINC000543782125.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000543782125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543782125/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000543782125 none COc1ccc(CCN(Cc2ccsc2)C(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 1, 14, 1, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 12, 7, 7, 4, 2, 4, 6, 11, 11, 11, 11, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 26, 24, 24, 24, 12, 12, 7, 7, 7, 7, 6, 6, 11, 11, 11, 1, 1, 1, 1, 1, 1, 12, 26, 26, 26] 50 rigid atoms, others: [50, 49, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 51, 52, 53, 54]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543782125 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000543782125 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543782125/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543782125/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543782125 Building ZINC000543792429 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543792429' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543792429 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000543792429 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543792429/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543792429 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 394) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/394 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/394' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCc1ccccc1c1ccc(Cn2ccnc2)cc1) `ZINC000543792429.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000543792429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543792429/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000543792429 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCc1ccccc1c1ccc(Cn2ccnc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 14, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 28, 50, 50, 50, 50, 20, 20, 2, 2, 2, 2, 2, 2, 3, 14, 14, 20, 20, 20, 20, 20, 20, 28, 28, 50, 50, 50, 20, 20] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543792429 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543792429/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543792429 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 395) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/395 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/395' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCc1ccccc1c1ccc(Cn2ccnc2)cc1) `ZINC000543792429.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000543792429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543792429/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000543792429 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCc1ccccc1c1ccc(Cn2ccnc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 14, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 28, 50, 50, 50, 50, 21, 21, 2, 2, 2, 2, 2, 2, 3, 14, 14, 21, 21, 21, 21, 21, 21, 28, 28, 50, 50, 50, 21, 21] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543792429 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000543792429 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543792429/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543792429/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543792429 Building ZINC000543792429 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543792429' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543792429 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000543792429 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543792429/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543792429 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 394) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/394: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCc1ccccc1c1ccc(Cn2ccnc2)cc1) `ZINC000543792429.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000543792429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543792429/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000543792429 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCc1ccccc1c1ccc(Cn2ccnc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 14, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 28, 50, 50, 50, 50, 20, 20, 2, 2, 2, 2, 2, 2, 3, 14, 14, 20, 20, 20, 20, 20, 20, 28, 28, 50, 50, 50, 20, 20] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543792429 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543792429/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543792429 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 395) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/395: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCc1ccccc1c1ccc(Cn2ccnc2)cc1) `ZINC000543792429.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000543792429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543792429/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000543792429 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCc1ccccc1c1ccc(Cn2ccnc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 14, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 28, 50, 50, 50, 50, 21, 21, 2, 2, 2, 2, 2, 2, 3, 14, 14, 21, 21, 21, 21, 21, 21, 28, 28, 50, 50, 50, 21, 21] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543792429 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000543792429 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543792429/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543792429/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543792429 Building ZINC001275890333 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275890333' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275890333 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001275890333 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275890333/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275890333 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 396) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/396 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/396' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(Oc2ccccc2CCNC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc1) `ZINC001275890333.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001275890333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275890333/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001275890333 none Cc1ccc(Oc2ccccc2CCNC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 33, 21, 21, 21, 21, 21, 21, 17, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 34, 34, 34, 34, 34, 34, 34, 21, 21, 21, 21, 17, 17, 11, 11, 2, 6, 6, 6, 6, 6, 6, 6, 34, 34] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275890333 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275890333/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275890333 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 397) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/397 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/397' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(Oc2ccccc2CCNC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc1) `ZINC001275890333.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001275890333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275890333/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001275890333 none Cc1ccc(Oc2ccccc2CCNC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 34, 33, 21, 21, 21, 21, 21, 21, 17, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 34, 34, 34, 34, 34, 34, 34, 21, 21, 21, 21, 17, 17, 11, 11, 2, 6, 6, 6, 6, 6, 6, 6, 34, 34] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275890333 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001275890333 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275890333/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275890333/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275890333 Building ZINC001275890333 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275890333' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275890333 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001275890333 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275890333/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275890333 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 396) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/396: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(Oc2ccccc2CCNC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc1) `ZINC001275890333.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001275890333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275890333/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001275890333 none Cc1ccc(Oc2ccccc2CCNC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 33, 21, 21, 21, 21, 21, 21, 17, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 34, 34, 34, 34, 34, 34, 34, 21, 21, 21, 21, 17, 17, 11, 11, 2, 6, 6, 6, 6, 6, 6, 6, 34, 34] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275890333 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275890333/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275890333 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 397) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/397: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(Oc2ccccc2CCNC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc1) `ZINC001275890333.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001275890333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275890333/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001275890333 none Cc1ccc(Oc2ccccc2CCNC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 34, 33, 21, 21, 21, 21, 21, 21, 17, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 34, 34, 34, 34, 34, 34, 34, 21, 21, 21, 21, 17, 17, 11, 11, 2, 6, 6, 6, 6, 6, 6, 6, 34, 34] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275890333 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001275890333 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275890333/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275890333/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275890333 Building ZINC001275924823 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275924823' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275924823 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001275924823 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275924823/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275924823 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 398) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/398 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/398' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)Cc1ccc(C)c(C)c1) `ZINC001275924823.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001275924823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275924823/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001275924823 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)Cc1ccc(C)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 3, 10, 10, 10, 10, 10, 10, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 6, 12, 12, 12, 12, 12, 12, 12, 3, 3, 3, 10, 10, 3, 10, 3, 3, 3, 3, 3, 3, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275924823 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275924823/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275924823 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 399) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/399 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/399' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)Cc1ccc(C)c(C)c1) `ZINC001275924823.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001275924823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275924823/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001275924823 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)Cc1ccc(C)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 3, 10, 10, 10, 10, 10, 10, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 6, 12, 12, 12, 12, 12, 12, 12, 3, 3, 3, 10, 10, 3, 10, 3, 3, 3, 3, 3, 3, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275924823 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001275924823 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275924823/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275924823/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275924823 Building ZINC001275924823 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275924823' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275924823 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001275924823 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275924823/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275924823 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 398) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/398: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)Cc1ccc(C)c(C)c1) `ZINC001275924823.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001275924823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275924823/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001275924823 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)Cc1ccc(C)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 3, 10, 10, 10, 10, 10, 10, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 6, 12, 12, 12, 12, 12, 12, 12, 3, 3, 3, 10, 10, 3, 10, 3, 3, 3, 3, 3, 3, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275924823 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275924823/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275924823 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 399) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/399: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)Cc1ccc(C)c(C)c1) `ZINC001275924823.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001275924823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275924823/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001275924823 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)Cc1ccc(C)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 3, 10, 10, 10, 10, 10, 10, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 6, 12, 12, 12, 12, 12, 12, 12, 3, 3, 3, 10, 10, 3, 10, 3, 3, 3, 3, 3, 3, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275924823 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001275924823 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275924823/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275924823/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001275924823 Building ZINC000543801571 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543801571' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543801571 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000543801571 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543801571/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543801571 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 400) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/400 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/400' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCS(=O)(=O)c1ccccc1Oc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)cc1) `ZINC000543801571.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000543801571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543801571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC000543801571 none CCS(=O)(=O)c1ccccc1Oc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 50, 50, 32, 32, 32, 32, 32, 32, 12, 6, 12, 12, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 12, 12, 50, 50, 50, 50, 50, 32, 32, 32, 32, 12, 12, 3, 2, 2, 2, 2, 2, 2, 12, 12] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543801571 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543801571/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543801571 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 401) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/401 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/401' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCS(=O)(=O)c1ccccc1Oc1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)cc1) `ZINC000543801571.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000543801571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543801571/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC000543801571 none CCS(=O)(=O)c1ccccc1Oc1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 34, 50, 50, 34, 34, 34, 34, 34, 34, 3, 6, 12, 12, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 12, 12, 50, 50, 50, 50, 50, 34, 34, 34, 34, 12, 12, 3, 2, 2, 2, 2, 2, 2, 12, 12] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543801571 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000543801571 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543801571/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543801571/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543801571 Building ZINC000543801571 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543801571' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543801571 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000543801571 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543801571/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543801571 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 400) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/400: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCS(=O)(=O)c1ccccc1Oc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)cc1) `ZINC000543801571.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000543801571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543801571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC000543801571 none CCS(=O)(=O)c1ccccc1Oc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 50, 50, 32, 32, 32, 32, 32, 32, 12, 6, 12, 12, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 12, 12, 50, 50, 50, 50, 50, 32, 32, 32, 32, 12, 12, 3, 2, 2, 2, 2, 2, 2, 12, 12] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543801571 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543801571/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543801571 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 401) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/401: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCS(=O)(=O)c1ccccc1Oc1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)cc1) `ZINC000543801571.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000543801571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543801571/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC000543801571 none CCS(=O)(=O)c1ccccc1Oc1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 34, 50, 50, 34, 34, 34, 34, 34, 34, 3, 6, 12, 12, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 12, 12, 50, 50, 50, 50, 50, 34, 34, 34, 34, 12, 12, 3, 2, 2, 2, 2, 2, 2, 12, 12] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543801571 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000543801571 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543801571/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543801571/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543801571 Building ZINC001276036279 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276036279' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276036279 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001276036279 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276036279/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276036279 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 402) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/402 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/402' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nnc(COc2ccc(Cl)cc2)s1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001276036279.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001276036279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276036279/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001276036279 none O=C(Nc1nnc(COc2ccc(Cl)cc2)s1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 14, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 8, 8, 8, 8, 31, 45, 45, 45, 45, 45, 45, 45, 8, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 4, 31, 31, 45, 45, 45, 45, 4, 2, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 139 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276036279 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276036279/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276036279 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 403) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/403 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/403' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nnc(COc2ccc(Cl)cc2)s1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001276036279.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001276036279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276036279/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001276036279 none O=C(Nc1nnc(COc2ccc(Cl)cc2)s1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 14, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 7, 7, 7, 7, 29, 44, 44, 44, 44, 44, 44, 44, 7, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 4, 29, 29, 44, 44, 44, 44, 4, 1, 4] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 130 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276036279 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001276036279 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276036279/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276036279/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276036279 Building ZINC001276036279 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276036279' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276036279 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001276036279 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276036279/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276036279 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 402) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/402: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nnc(COc2ccc(Cl)cc2)s1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001276036279.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001276036279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276036279/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001276036279 none O=C(Nc1nnc(COc2ccc(Cl)cc2)s1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 14, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 8, 8, 8, 8, 31, 45, 45, 45, 45, 45, 45, 45, 8, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 4, 31, 31, 45, 45, 45, 45, 4, 2, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 139 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276036279 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276036279/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276036279 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 403) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/403: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nnc(COc2ccc(Cl)cc2)s1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001276036279.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001276036279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276036279/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001276036279 none O=C(Nc1nnc(COc2ccc(Cl)cc2)s1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 14, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 7, 7, 7, 7, 29, 44, 44, 44, 44, 44, 44, 44, 7, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 4, 29, 29, 44, 44, 44, 44, 4, 1, 4] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 130 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276036279 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001276036279 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276036279/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276036279/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276036279 Building ZINC000410094658 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410094658' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410094658 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000410094658 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410094658/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410094658 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 404) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/404 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/404' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nnc(c2cc(Br)ccc2F)s1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000410094658.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000410094658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410094658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000410094658 none O=C(Nc1nnc(c2cc(Br)ccc2F)s1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 15, 14, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 9, 9, 9, 9, 38, 38, 38, 38, 38, 38, 38, 9, 1, 1, 1, 4, 4, 1, 1, 4, 4, 6, 38, 38, 38, 4, 4, 4, 4] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410094658 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410094658/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410094658 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 405) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/405 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/405' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nnc(c2cc(Br)ccc2F)s1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000410094658.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000410094658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410094658/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000410094658 none O=C(Nc1nnc(c2cc(Br)ccc2F)s1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 15, 14, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 10, 10, 10, 10, 38, 38, 38, 38, 38, 38, 38, 10, 1, 1, 1, 4, 4, 1, 1, 4, 4, 6, 38, 38, 38, 4, 4, 4, 4] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410094658 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000410094658 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410094658/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410094658/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410094658 Building ZINC000410094658 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410094658' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410094658 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000410094658 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410094658/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410094658 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 404) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/404: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nnc(c2cc(Br)ccc2F)s1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000410094658.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000410094658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410094658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000410094658 none O=C(Nc1nnc(c2cc(Br)ccc2F)s1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 15, 14, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 9, 9, 9, 9, 38, 38, 38, 38, 38, 38, 38, 9, 1, 1, 1, 4, 4, 1, 1, 4, 4, 6, 38, 38, 38, 4, 4, 4, 4] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410094658 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410094658/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410094658 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 405) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/405: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nnc(c2cc(Br)ccc2F)s1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000410094658.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000410094658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410094658/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000410094658 none O=C(Nc1nnc(c2cc(Br)ccc2F)s1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 15, 14, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 10, 10, 10, 10, 38, 38, 38, 38, 38, 38, 38, 10, 1, 1, 1, 4, 4, 1, 1, 4, 4, 6, 38, 38, 38, 4, 4, 4, 4] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410094658 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000410094658 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410094658/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410094658/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410094658 Building ZINC000410110511 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410110511' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410110511 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000410110511 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410110511/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410110511 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 406) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/406 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/406' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(F)(c2ccccc2C(F)(F)F)CC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000410110511.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000410110511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410110511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC000410110511 none O=C(N1CCC(F)(c2ccccc2C(F)(F)F)CC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 15, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 1, 14, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 6, 6, 6, 6, 8, 8, 6, 8, 8, 6, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 8, 8, 6, 8, 8, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 54 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410110511 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410110511/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410110511 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 407) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/407 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/407' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(F)(c2ccccc2C(F)(F)F)CC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000410110511.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000410110511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410110511/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC000410110511 none O=C(N1CCC(F)(c2ccccc2C(F)(F)F)CC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 15, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 6, 6, 6, 6, 8, 8, 6, 8, 8, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 8, 8, 6, 8, 8, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 47 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410110511 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000410110511 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410110511/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410110511/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410110511 Building ZINC000410110511 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410110511' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410110511 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000410110511 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410110511/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410110511 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 406) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/406: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(F)(c2ccccc2C(F)(F)F)CC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000410110511.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000410110511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410110511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC000410110511 none O=C(N1CCC(F)(c2ccccc2C(F)(F)F)CC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 15, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 1, 14, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 6, 6, 6, 6, 8, 8, 6, 8, 8, 6, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 8, 8, 6, 8, 8, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 54 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410110511 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410110511/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410110511 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 407) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/407: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(F)(c2ccccc2C(F)(F)F)CC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000410110511.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000410110511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410110511/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC000410110511 none O=C(N1CCC(F)(c2ccccc2C(F)(F)F)CC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 15, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 6, 6, 6, 6, 8, 8, 6, 8, 8, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 8, 8, 6, 8, 8, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 47 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410110511 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000410110511 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410110511/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410110511/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410110511 Building ZINC000410330533 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410330533' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410330533 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000410330533 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410330533/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410330533 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 408) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/408 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/408' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)c1nc(c2ccccc2)cs1) `ZINC000410330533.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000410330533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410330533/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000410330533 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)c1nc(c2ccccc2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 3, 3, 2, 3, 3, 2, 2, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 26, 26, 26, 50, 50, 48, 50, 50, 26, 26, 2, 2, 2, 3, 3, 2, 3, 3, 2, 2, 2, 3, 5, 5, 5, 50, 50, 50, 50, 50, 26] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410330533 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410330533/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410330533 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 409) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/409 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/409' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)c1nc(c2ccccc2)cs1) `ZINC000410330533.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000410330533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410330533/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000410330533 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)c1nc(c2ccccc2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 25, 25, 25, 45, 45, 28, 45, 45, 25, 25, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 6, 6, 6, 45, 45, 45, 45, 45, 25] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410330533 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000410330533 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410330533/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410330533/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410330533 Building ZINC000410330533 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410330533' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410330533 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000410330533 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410330533/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410330533 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 408) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/408: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)c1nc(c2ccccc2)cs1) `ZINC000410330533.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000410330533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410330533/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000410330533 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)c1nc(c2ccccc2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 3, 3, 2, 3, 3, 2, 2, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 26, 26, 26, 50, 50, 48, 50, 50, 26, 26, 2, 2, 2, 3, 3, 2, 3, 3, 2, 2, 2, 3, 5, 5, 5, 50, 50, 50, 50, 50, 26] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410330533 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410330533/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410330533 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 409) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/409: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)c1nc(c2ccccc2)cs1) `ZINC000410330533.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000410330533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410330533/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000410330533 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)c1nc(c2ccccc2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 25, 25, 25, 45, 45, 28, 45, 45, 25, 25, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 6, 6, 6, 45, 45, 45, 45, 45, 25] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410330533 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000410330533 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410330533/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410330533/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410330533 Building ZINC000410330534 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410330534' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410330534 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000410330534 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410330534/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410330534 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 410) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/410 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/410' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)c1nc(c2ccccc2)cs1) `ZINC000410330534.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000410330534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410330534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000410330534 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)c1nc(c2ccccc2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 24, 24, 24, 43, 43, 43, 43, 43, 24, 24, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 5, 5, 5, 43, 43, 43, 43, 43, 24] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410330534 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410330534/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410330534 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 411) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/411 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/411' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)c1nc(c2ccccc2)cs1) `ZINC000410330534.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000410330534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410330534/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000410330534 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)c1nc(c2ccccc2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 26, 26, 26, 50, 50, 26, 50, 50, 26, 26, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 5, 5, 5, 50, 50, 26, 50, 50, 26] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410330534 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000410330534 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410330534/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410330534/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410330534 Building ZINC000410330534 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410330534' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410330534 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000410330534 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410330534/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410330534 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 410) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/410: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)c1nc(c2ccccc2)cs1) `ZINC000410330534.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000410330534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410330534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000410330534 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)c1nc(c2ccccc2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 24, 24, 24, 43, 43, 43, 43, 43, 24, 24, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 5, 5, 5, 43, 43, 43, 43, 43, 24] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410330534 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410330534/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410330534 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 411) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/411: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)c1nc(c2ccccc2)cs1) `ZINC000410330534.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000410330534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410330534/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000410330534 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)c1nc(c2ccccc2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 26, 26, 26, 50, 50, 26, 50, 50, 26, 26, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 5, 5, 5, 50, 50, 26, 50, 50, 26] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410330534 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000410330534 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410330534/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410330534/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000410330534 Building ZINC001276240987 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276240987' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276240987 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001276240987 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276240987/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276240987 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 412) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/412 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/412' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(Cc1occc1C)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001276240987.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001276240987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276240987/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001276240987 none CCN(Cc1occc1C)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 12, 1, 1, 1, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 7, 7, 7, 7, 7, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 3, 3, 3, 3, 3, 4, 4, 7, 7, 7, 7, 7, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276240987 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276240987/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276240987 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 413) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/413 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/413' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(Cc1occc1C)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001276240987.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001276240987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276240987/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001276240987 none CCN(Cc1occc1C)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 12, 1, 1, 1, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 7, 7, 7, 7, 7, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 3, 3, 3, 3, 3, 4, 4, 7, 7, 7, 7, 7, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276240987 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001276240987 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276240987/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276240987/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276240987 Building ZINC001276240987 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276240987' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276240987 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001276240987 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276240987/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276240987 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 412) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/412: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(Cc1occc1C)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001276240987.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001276240987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276240987/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001276240987 none CCN(Cc1occc1C)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 12, 1, 1, 1, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 7, 7, 7, 7, 7, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 3, 3, 3, 3, 3, 4, 4, 7, 7, 7, 7, 7, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276240987 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276240987/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276240987 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 413) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/413: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(Cc1occc1C)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001276240987.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001276240987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276240987/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001276240987 none CCN(Cc1occc1C)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 12, 1, 1, 1, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 7, 7, 7, 7, 7, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 3, 3, 3, 3, 3, 4, 4, 7, 7, 7, 7, 7, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276240987 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001276240987 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276240987/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276240987/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276240987 Building ZINC000466891110 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466891110' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466891110 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000466891110 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466891110/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466891110 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 414) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/414 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/414' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(N(C)C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1F) `ZINC000466891110.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000466891110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466891110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000466891110 none COc1ccc(N(C)C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 8, 8, 8, 12, 12, 12, 8, 8, 1, 1, 1, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2, 8] 50 rigid atoms, others: [11, 37, 38, 7, 8, 9, 10, 39, 12, 6, 5] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466891110 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466891110/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466891110 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 415) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/415 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/415' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(N(C)C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1F) `ZINC000466891110.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000466891110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466891110/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000466891110 none COc1ccc(N(C)C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 13, 13, 2, 13, 13, 13, 13, 13, 13, 2, 2, 6, 6, 6, 9, 9, 9, 6, 6, 1, 1, 1, 2, 2, 2, 13, 13, 2, 13, 2, 2, 2, 6] 50 rigid atoms, others: [11, 37, 38, 7, 8, 9, 10, 39, 12, 6, 5] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 42 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466891110 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000466891110 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466891110/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466891110/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466891110 Building ZINC000466891110 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466891110' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466891110 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000466891110 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466891110/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466891110 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 414) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/414: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(N(C)C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1F) `ZINC000466891110.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000466891110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466891110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000466891110 none COc1ccc(N(C)C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 8, 8, 8, 12, 12, 12, 8, 8, 1, 1, 1, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2, 8] 50 rigid atoms, others: [11, 37, 38, 7, 8, 9, 10, 39, 12, 6, 5] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466891110 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466891110/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466891110 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 415) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/415: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(N(C)C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1F) `ZINC000466891110.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000466891110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466891110/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000466891110 none COc1ccc(N(C)C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 13, 13, 2, 13, 13, 13, 13, 13, 13, 2, 2, 6, 6, 6, 9, 9, 9, 6, 6, 1, 1, 1, 2, 2, 2, 13, 13, 2, 13, 2, 2, 2, 6] 50 rigid atoms, others: [11, 37, 38, 7, 8, 9, 10, 39, 12, 6, 5] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 42 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466891110 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000466891110 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466891110/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466891110/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000466891110 Building ZINC000543830948 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543830948' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543830948 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000543830948 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543830948/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543830948 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 416) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/416 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/416' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCc2c(cccc2NC(=O)Nc2ccccc2)C1) `ZINC000543830948.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000543830948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543830948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000543830948 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCc2c(cccc2NC(=O)Nc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 2, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 29, 30, 30, 38, 50, 50, 38, 50, 50, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 29, 38, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 34, 3, 32, 33, 6, 7, 8, 9, 10, 2, 35, 4, 5, 37, 36] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543830948 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543830948/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543830948 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 417) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/417 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/417' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCc2c(cccc2NC(=O)Nc2ccccc2)C1) `ZINC000543830948.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000543830948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543830948/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000543830948 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCc2c(cccc2NC(=O)Nc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 2, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 29, 31, 31, 39, 50, 50, 50, 50, 50, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 29, 39, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 34, 3, 32, 33, 6, 7, 8, 9, 10, 2, 35, 4, 5, 37, 36] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543830948 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000543830948 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543830948/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543830948/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543830948 Building ZINC000543830948 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543830948' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543830948 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000543830948 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543830948/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543830948 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 416) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/416: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCc2c(cccc2NC(=O)Nc2ccccc2)C1) `ZINC000543830948.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000543830948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543830948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000543830948 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCc2c(cccc2NC(=O)Nc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 2, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 29, 30, 30, 38, 50, 50, 38, 50, 50, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 29, 38, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 34, 3, 32, 33, 6, 7, 8, 9, 10, 2, 35, 4, 5, 37, 36] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543830948 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543830948/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543830948 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 417) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/417: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCc2c(cccc2NC(=O)Nc2ccccc2)C1) `ZINC000543830948.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000543830948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543830948/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000543830948 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCc2c(cccc2NC(=O)Nc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 2, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 29, 31, 31, 39, 50, 50, 50, 50, 50, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 29, 39, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 34, 3, 32, 33, 6, 7, 8, 9, 10, 2, 35, 4, 5, 37, 36] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543830948 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000543830948 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543830948/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543830948/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000543830948 Building ZINC000544399355 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544399355' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544399355 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000544399355 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544399355/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544399355 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 418) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/418 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/418' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(C2CC2)c1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000544399355.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000544399355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544399355/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000544399355 none Cc1noc(C2CC2)c1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 14, 14, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 16, 16, 3, 16, 16, 16, 16, 16, 16, 3, 3, 7, 7, 7, 14, 14, 14, 14, 14, 2, 3, 3, 3, 16, 16, 3, 16, 3, 3, 3] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544399355 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544399355/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544399355 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 419) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/419 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/419' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(C2CC2)c1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000544399355.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000544399355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544399355/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000544399355 none Cc1noc(C2CC2)c1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 17, 17, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 16, 16, 3, 16, 16, 16, 16, 16, 16, 3, 3, 8, 8, 8, 17, 17, 17, 17, 17, 2, 3, 3, 3, 16, 16, 3, 16, 3, 3, 3] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544399355 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000544399355 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544399355/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544399355/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544399355 Building ZINC000544399355 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544399355' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544399355 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000544399355 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544399355/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544399355 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 418) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/418: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(C2CC2)c1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000544399355.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000544399355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544399355/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000544399355 none Cc1noc(C2CC2)c1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 14, 14, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 16, 16, 3, 16, 16, 16, 16, 16, 16, 3, 3, 7, 7, 7, 14, 14, 14, 14, 14, 2, 3, 3, 3, 16, 16, 3, 16, 3, 3, 3] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544399355 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544399355/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544399355 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 419) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/419: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(C2CC2)c1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000544399355.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000544399355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544399355/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000544399355 none Cc1noc(C2CC2)c1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 17, 17, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 16, 16, 3, 16, 16, 16, 16, 16, 16, 3, 3, 8, 8, 8, 17, 17, 17, 17, 17, 2, 3, 3, 3, 16, 16, 3, 16, 3, 3, 3] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544399355 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000544399355 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544399355/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544399355/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544399355 Building ZINC000544764939 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544764939' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544764939 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000544764939 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544764939/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544764939 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 420) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/420 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/420' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C(=O)c2c(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)sc3c2CCOC3)cc1) `ZINC000544764939.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000544764939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544764939/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000544764939 none Cc1ccc(C(=O)c2c(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)sc3c2CCOC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 14, 1, 1, 5, 5, 12, 5, 1, 1, 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, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 42, 28, 42, 28, 6, 6, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 28, 28, 28, 28, 28, 28, 28, 42, 42, 42, 42, 42, 42, 42, 6, 4, 4, 4, 4, 28, 28, 28, 28, 28, 28, 42, 42] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544764939 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544764939/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544764939 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 421) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/421 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/421' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C(=O)c2c(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)sc3c2CCOC3)cc1) `ZINC000544764939.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000544764939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544764939/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000544764939 none Cc1ccc(C(=O)c2c(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)sc3c2CCOC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 14, 1, 1, 5, 5, 12, 5, 1, 1, 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, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 43, 31, 43, 31, 7, 7, 1, 7, 1, 1, 1, 6, 6, 1, 1, 6, 6, 31, 31, 31, 31, 31, 31, 31, 43, 43, 43, 43, 43, 43, 43, 7, 6, 6, 6, 6, 31, 31, 31, 31, 31, 31, 43, 43] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544764939 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000544764939 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544764939/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544764939/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544764939 Building ZINC000544764939 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544764939' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544764939 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000544764939 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544764939/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544764939 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 420) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/420: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C(=O)c2c(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)sc3c2CCOC3)cc1) `ZINC000544764939.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000544764939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544764939/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000544764939 none Cc1ccc(C(=O)c2c(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)sc3c2CCOC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 14, 1, 1, 5, 5, 12, 5, 1, 1, 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, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 42, 28, 42, 28, 6, 6, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 28, 28, 28, 28, 28, 28, 28, 42, 42, 42, 42, 42, 42, 42, 6, 4, 4, 4, 4, 28, 28, 28, 28, 28, 28, 42, 42] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544764939 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544764939/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544764939 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 421) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/421: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C(=O)c2c(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)sc3c2CCOC3)cc1) `ZINC000544764939.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000544764939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544764939/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000544764939 none Cc1ccc(C(=O)c2c(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)sc3c2CCOC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 14, 1, 1, 5, 5, 12, 5, 1, 1, 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, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 43, 31, 43, 31, 7, 7, 1, 7, 1, 1, 1, 6, 6, 1, 1, 6, 6, 31, 31, 31, 31, 31, 31, 31, 43, 43, 43, 43, 43, 43, 43, 7, 6, 6, 6, 6, 31, 31, 31, 31, 31, 31, 43, 43] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544764939 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000544764939 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544764939/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544764939/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544764939 Building ZINC000544814847 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544814847' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544814847 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000544814847 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544814847/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544814847 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 422) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/422 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/422' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1nc(c2ccc(Br)cc2)c(C)s1) `ZINC000544814847.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000544814847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544814847/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000544814847 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1nc(c2ccc(Br)cc2)c(C)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 9, 9, 9, 1, 9, 9, 1, 1, 1, 1, 10, 10, 10, 17, 17, 17, 30, 30, 25, 30, 30, 30, 17, 17, 17, 10, 10, 10, 9, 9, 9, 9, 10, 30, 30, 30, 30, 17, 17, 17] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 111 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544814847 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544814847/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544814847 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 423) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/423 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/423' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1nc(c2ccc(Br)cc2)c(C)s1) `ZINC000544814847.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000544814847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544814847/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000544814847 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1nc(c2ccc(Br)cc2)c(C)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 9, 9, 9, 1, 9, 9, 1, 1, 1, 1, 10, 10, 10, 18, 18, 18, 30, 30, 18, 25, 30, 30, 18, 18, 18, 10, 10, 10, 9, 9, 9, 9, 10, 30, 30, 30, 30, 18, 18, 18] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544814847 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000544814847 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544814847/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544814847/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544814847 Building ZINC000544814847 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544814847' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544814847 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000544814847 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544814847/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544814847 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 422) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/422: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1nc(c2ccc(Br)cc2)c(C)s1) `ZINC000544814847.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000544814847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544814847/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000544814847 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1nc(c2ccc(Br)cc2)c(C)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 9, 9, 9, 1, 9, 9, 1, 1, 1, 1, 10, 10, 10, 17, 17, 17, 30, 30, 25, 30, 30, 30, 17, 17, 17, 10, 10, 10, 9, 9, 9, 9, 10, 30, 30, 30, 30, 17, 17, 17] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 111 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544814847 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544814847/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544814847 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 423) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/423: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1nc(c2ccc(Br)cc2)c(C)s1) `ZINC000544814847.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000544814847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544814847/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000544814847 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1nc(c2ccc(Br)cc2)c(C)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 9, 9, 9, 1, 9, 9, 1, 1, 1, 1, 10, 10, 10, 18, 18, 18, 30, 30, 18, 25, 30, 30, 18, 18, 18, 10, 10, 10, 9, 9, 9, 9, 10, 30, 30, 30, 30, 18, 18, 18] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544814847 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000544814847 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544814847/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544814847/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544814847 Building ZINC000544816688 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816688' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816688 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000544816688 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816688/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816688 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 424) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/424 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/424' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(Cc1nnc(c2ccccc2Cl)o1)C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC000544816688.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000544816688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816688/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC000544816688 none CCCN(Cc1nnc(c2ccccc2Cl)o1)C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', '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, 8, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 16, 12, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [4, 4, 2, 1, 2, 5, 11, 11, 11, 11, 27, 27, 13, 27, 27, 27, 11, 1, 1, 1, 1, 1, 4, 4, 2, 4, 7, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 27, 27, 19, 27, 4, 4, 7, 7, 7, 4] 50 rigid atoms, others: [3, 17, 18, 19, 20, 21] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 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: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816688 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816688/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816688 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 425) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/425 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/425' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(Cc1nnc(c2ccccc2Cl)o1)C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC000544816688.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000544816688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816688/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC000544816688 none CCCN(Cc1nnc(c2ccccc2Cl)o1)C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', '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, 8, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 16, 12, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [4, 4, 2, 1, 2, 5, 12, 12, 12, 12, 27, 27, 14, 27, 27, 27, 12, 1, 1, 1, 1, 1, 4, 4, 2, 4, 6, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 27, 27, 19, 27, 4, 4, 6, 6, 6, 4] 50 rigid atoms, others: [3, 17, 18, 19, 20, 21] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 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: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816688 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000544816688 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816688/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816688/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816688 Building ZINC000544816688 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816688' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816688 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000544816688 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816688/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816688 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 424) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/424: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(Cc1nnc(c2ccccc2Cl)o1)C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC000544816688.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000544816688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816688/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC000544816688 none CCCN(Cc1nnc(c2ccccc2Cl)o1)C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', '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, 8, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 16, 12, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [4, 4, 2, 1, 2, 5, 11, 11, 11, 11, 27, 27, 13, 27, 27, 27, 11, 1, 1, 1, 1, 1, 4, 4, 2, 4, 7, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 27, 27, 19, 27, 4, 4, 7, 7, 7, 4] 50 rigid atoms, others: [3, 17, 18, 19, 20, 21] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 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: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816688 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816688/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816688 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 425) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/425: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(Cc1nnc(c2ccccc2Cl)o1)C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC000544816688.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000544816688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816688/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC000544816688 none CCCN(Cc1nnc(c2ccccc2Cl)o1)C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', '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, 8, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 16, 12, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [4, 4, 2, 1, 2, 5, 12, 12, 12, 12, 27, 27, 14, 27, 27, 27, 12, 1, 1, 1, 1, 1, 4, 4, 2, 4, 6, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 27, 27, 19, 27, 4, 4, 6, 6, 6, 4] 50 rigid atoms, others: [3, 17, 18, 19, 20, 21] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 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: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816688 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000544816688 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816688/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816688/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816688 Building ZINC000544816400 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816400' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816400 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000544816400 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816400/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816400 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 426) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/426 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/426' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)[C@H](C)c1cccc(C(F)(F)F)c1) `ZINC000544816400.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000544816400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000544816400 none COCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)[C@H](C)c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 7, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 5, 2, 2, 2, 2, 3, 3, 3, 15, 15, 6, 15, 15, 15, 15, 15, 15, 6, 6, 6, 4, 4, 4, 4, 2, 2, 5, 5, 5, 2, 3, 3, 3, 15, 15, 6, 15] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 63 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816400 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816400/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816400 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 427) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/427 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/427' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)[C@H](C)c1cccc(C(F)(F)F)c1) `ZINC000544816400.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000544816400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816400/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000544816400 none COCCN(C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)[C@H](C)c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 7, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 2, 1, 1, 1, 2, 2, 2, 2, 4, 2, 2, 2, 3, 3, 3, 3, 11, 11, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 7, 7, 7, 2, 2, 4, 4, 4, 2, 3, 3, 3, 11, 11, 5, 11] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 65 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816400 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000544816400 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816400/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816400/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816400 Building ZINC000544816400 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816400' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816400 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000544816400 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816400/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816400 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 426) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/426: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)[C@H](C)c1cccc(C(F)(F)F)c1) `ZINC000544816400.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000544816400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000544816400 none COCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)[C@H](C)c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 7, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 5, 2, 2, 2, 2, 3, 3, 3, 15, 15, 6, 15, 15, 15, 15, 15, 15, 6, 6, 6, 4, 4, 4, 4, 2, 2, 5, 5, 5, 2, 3, 3, 3, 15, 15, 6, 15] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 63 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816400 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816400/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816400 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 427) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/427: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)[C@H](C)c1cccc(C(F)(F)F)c1) `ZINC000544816400.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000544816400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816400/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000544816400 none COCCN(C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)[C@H](C)c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 7, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 2, 1, 1, 1, 2, 2, 2, 2, 4, 2, 2, 2, 3, 3, 3, 3, 11, 11, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 7, 7, 7, 2, 2, 4, 4, 4, 2, 3, 3, 3, 11, 11, 5, 11] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 65 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816400 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000544816400 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816400/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816400/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816400 Building ZINC000544816401 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816401' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816401 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000544816401 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816401/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816401 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 428) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/428 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/428' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)[C@@H](C)c1cccc(C(F)(F)F)c1) `ZINC000544816401.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000544816401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000544816401 none COCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)[C@@H](C)c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 7, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 4, 2, 2, 2, 2, 2, 2, 2, 10, 10, 4, 10, 10, 10, 10, 10, 10, 9, 9, 9, 6, 6, 6, 6, 2, 2, 4, 4, 4, 2, 2, 2, 2, 10, 10, 4, 10] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 59 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816401 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816401/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816401 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 429) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/429 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/429' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)[C@@H](C)c1cccc(C(F)(F)F)c1) `ZINC000544816401.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000544816401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816401/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000544816401 none COCCN(C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)[C@@H](C)c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 7, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 4, 2, 2, 2, 2, 3, 3, 3, 16, 16, 6, 16, 16, 16, 16, 16, 16, 6, 6, 6, 4, 4, 4, 4, 2, 2, 4, 4, 4, 2, 3, 3, 3, 16, 16, 6, 16] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 66 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816401 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000544816401 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816401/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816401/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816401 Building ZINC000544816401 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816401' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816401 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000544816401 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816401/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816401 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 428) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/428: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)[C@@H](C)c1cccc(C(F)(F)F)c1) `ZINC000544816401.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000544816401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000544816401 none COCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)[C@@H](C)c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 7, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 4, 2, 2, 2, 2, 2, 2, 2, 10, 10, 4, 10, 10, 10, 10, 10, 10, 9, 9, 9, 6, 6, 6, 6, 2, 2, 4, 4, 4, 2, 2, 2, 2, 10, 10, 4, 10] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 59 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816401 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816401/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816401 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 429) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/429: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)[C@@H](C)c1cccc(C(F)(F)F)c1) `ZINC000544816401.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000544816401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816401/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000544816401 none COCCN(C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)[C@@H](C)c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 7, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 4, 2, 2, 2, 2, 3, 3, 3, 16, 16, 6, 16, 16, 16, 16, 16, 16, 6, 6, 6, 4, 4, 4, 4, 2, 2, 4, 4, 4, 2, 3, 3, 3, 16, 16, 6, 16] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 66 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816401 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000544816401 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816401/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816401/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544816401 Building ZINC000544823103 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544823103' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544823103 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000544823103 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544823103/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544823103 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 430) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/430 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/430' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(F)c(NC(=O)C3CCCCC3)c2)cc1Cl) `ZINC000544823103.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000544823103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544823103/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000544823103 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(F)c(NC(=O)C3CCCCC3)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 6, 6, 10, 28, 28, 28, 28, 28, 4, 2, 2, 2, 4, 4, 4, 2, 2, 1, 4, 4, 6, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 4, 2] 50 rigid atoms, others: [35, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544823103 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544823103/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544823103 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 431) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/431 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/431' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(F)c(NC(=O)C3CCCCC3)c2)cc1Cl) `ZINC000544823103.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000544823103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544823103/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000544823103 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(F)c(NC(=O)C3CCCCC3)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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: [6, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 6, 6, 9, 27, 27, 27, 27, 27, 5, 4, 4, 4, 6, 6, 6, 4, 4, 2, 5, 5, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 5, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544823103 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000544823103 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544823103/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544823103/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544823103 Building ZINC000544823103 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544823103' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544823103 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000544823103 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544823103/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544823103 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 430) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/430: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(F)c(NC(=O)C3CCCCC3)c2)cc1Cl) `ZINC000544823103.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000544823103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544823103/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000544823103 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(F)c(NC(=O)C3CCCCC3)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 6, 6, 10, 28, 28, 28, 28, 28, 4, 2, 2, 2, 4, 4, 4, 2, 2, 1, 4, 4, 6, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 4, 2] 50 rigid atoms, others: [35, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544823103 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544823103/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544823103 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 431) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/431: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(F)c(NC(=O)C3CCCCC3)c2)cc1Cl) `ZINC000544823103.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000544823103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544823103/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000544823103 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(F)c(NC(=O)C3CCCCC3)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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: [6, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 6, 6, 9, 27, 27, 27, 27, 27, 5, 4, 4, 4, 6, 6, 6, 4, 4, 2, 5, 5, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 5, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544823103 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000544823103 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544823103/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544823103/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544823103 Building ZINC000544830581 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544830581' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544830581 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000544830581 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544830581/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544830581 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 432) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/432 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/432' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(Sc3nnc(C)s3)cc2C)cc1Cl) `ZINC000544830581.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000544830581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544830581/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000544830581 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(Sc3nnc(C)s3)cc2C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 1, 8, 8, 1, 5, 14, 1, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 4, 18, 36, 36, 36, 36, 36, 4, 4, 4, 4, 4, 4, 9, 9, 9, 4, 4, 2, 4, 4, 36, 36, 36, 4, 4, 4, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544830581 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544830581/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544830581 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 433) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/433 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/433' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Sc3nnc(C)s3)cc2C)cc1Cl) `ZINC000544830581.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000544830581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544830581/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000544830581 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Sc3nnc(C)s3)cc2C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 1, 8, 8, 1, 5, 14, 1, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 4, 19, 34, 34, 34, 34, 34, 4, 4, 4, 4, 4, 4, 8, 8, 8, 4, 4, 2, 4, 4, 34, 34, 34, 4, 4, 4, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544830581 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000544830581 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544830581/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544830581/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544830581 Building ZINC000544830581 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544830581' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544830581 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000544830581 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544830581/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544830581 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 432) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/432: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(Sc3nnc(C)s3)cc2C)cc1Cl) `ZINC000544830581.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000544830581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544830581/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000544830581 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(Sc3nnc(C)s3)cc2C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 1, 8, 8, 1, 5, 14, 1, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 4, 18, 36, 36, 36, 36, 36, 4, 4, 4, 4, 4, 4, 9, 9, 9, 4, 4, 2, 4, 4, 36, 36, 36, 4, 4, 4, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544830581 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544830581/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544830581 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 433) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/433: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Sc3nnc(C)s3)cc2C)cc1Cl) `ZINC000544830581.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000544830581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544830581/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000544830581 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Sc3nnc(C)s3)cc2C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 1, 8, 8, 1, 5, 14, 1, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 4, 19, 34, 34, 34, 34, 34, 4, 4, 4, 4, 4, 4, 8, 8, 8, 4, 4, 2, 4, 4, 34, 34, 34, 4, 4, 4, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544830581 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000544830581 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544830581/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544830581/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544830581 Building ZINC000544847842 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544847842' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544847842 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000544847842 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544847842/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544847842 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 434) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/434 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/434' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc3nc(C(F)(F)C(F)(F)F)[nH]c3c2)cc1Cl) `ZINC000544847842.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000544847842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544847842/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000544847842 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc3nc(C(F)(F)C(F)(F)F)[nH]c3c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'F', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 5, 15, 15, 5, 15, 15, 15, 8, 6, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 28, 28, 28, 28, 28, 28, 6, 6, 6, 6, 4, 4, 4, 8, 8, 8, 4, 4, 2, 6, 6, 6, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544847842 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544847842/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544847842 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 435) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/435 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/435' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc3nc(C(F)(F)C(F)(F)F)[nH]c3c2)cc1Cl) `ZINC000544847842.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000544847842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544847842/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000544847842 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc3nc(C(F)(F)C(F)(F)F)[nH]c3c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'F', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 5, 15, 15, 5, 15, 15, 15, 8, 6, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 29, 29, 29, 29, 29, 29, 6, 6, 6, 6, 4, 4, 4, 8, 8, 8, 4, 4, 2, 6, 6, 6, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544847842 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000544847842 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544847842/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544847842/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544847842 Building ZINC000544847842 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544847842' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544847842 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000544847842 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544847842/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544847842 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 434) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/434: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc3nc(C(F)(F)C(F)(F)F)[nH]c3c2)cc1Cl) `ZINC000544847842.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000544847842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544847842/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000544847842 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc3nc(C(F)(F)C(F)(F)F)[nH]c3c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'F', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 5, 15, 15, 5, 15, 15, 15, 8, 6, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 28, 28, 28, 28, 28, 28, 6, 6, 6, 6, 4, 4, 4, 8, 8, 8, 4, 4, 2, 6, 6, 6, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544847842 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544847842/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544847842 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 435) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/435: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc3nc(C(F)(F)C(F)(F)F)[nH]c3c2)cc1Cl) `ZINC000544847842.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000544847842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544847842/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000544847842 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc3nc(C(F)(F)C(F)(F)F)[nH]c3c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'F', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 5, 15, 15, 5, 15, 15, 15, 8, 6, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 29, 29, 29, 29, 29, 29, 6, 6, 6, 6, 4, 4, 4, 8, 8, 8, 4, 4, 2, 6, 6, 6, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544847842 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000544847842 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544847842/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544847842/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544847842 Building ZINC000544849261 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544849261' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544849261 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000544849261 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544849261/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544849261 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 436) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/436 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/436' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](c2ccc(OC(F)F)cc2)C(F)(F)F)cc1Cl) `ZINC000544849261.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000544849261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544849261/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000544849261 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](c2ccc(OC(F)F)cc2)C(F)(F)F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 15, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 6, 6, 4, 4, 23, 27, 27, 6, 6, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 4, 4, 2, 6, 6, 27, 6, 6, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544849261 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544849261/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544849261 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 437) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/437 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/437' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](c2ccc(OC(F)F)cc2)C(F)(F)F)cc1Cl) `ZINC000544849261.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000544849261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544849261/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000544849261 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](c2ccc(OC(F)F)cc2)C(F)(F)F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 15, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 6, 6, 4, 4, 24, 26, 26, 6, 6, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 4, 4, 2, 6, 6, 26, 6, 6, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544849261 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000544849261 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544849261/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544849261/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544849261 Building ZINC000544849261 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544849261' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544849261 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000544849261 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544849261/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544849261 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 436) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/436: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](c2ccc(OC(F)F)cc2)C(F)(F)F)cc1Cl) `ZINC000544849261.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000544849261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544849261/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000544849261 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](c2ccc(OC(F)F)cc2)C(F)(F)F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 15, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 6, 6, 4, 4, 23, 27, 27, 6, 6, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 4, 4, 2, 6, 6, 27, 6, 6, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544849261 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544849261/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544849261 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 437) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/437: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](c2ccc(OC(F)F)cc2)C(F)(F)F)cc1Cl) `ZINC000544849261.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000544849261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544849261/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000544849261 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](c2ccc(OC(F)F)cc2)C(F)(F)F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 15, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 6, 6, 4, 4, 24, 26, 26, 6, 6, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 4, 4, 2, 6, 6, 26, 6, 6, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544849261 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000544849261 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544849261/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544849261/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544849261 Building ZINC000544849265 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544849265' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544849265 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000544849265 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544849265/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544849265 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 438) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/438 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/438' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](c2ccc(OC(F)F)cc2)C(F)(F)F)cc1Cl) `ZINC000544849265.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000544849265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544849265/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000544849265 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](c2ccc(OC(F)F)cc2)C(F)(F)F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 15, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 6, 6, 4, 4, 24, 27, 27, 6, 6, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 4, 4, 2, 6, 6, 27, 6, 6, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544849265 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544849265/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544849265 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 439) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/439 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/439' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](c2ccc(OC(F)F)cc2)C(F)(F)F)cc1Cl) `ZINC000544849265.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000544849265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544849265/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000544849265 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](c2ccc(OC(F)F)cc2)C(F)(F)F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 15, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 6, 6, 4, 4, 23, 27, 27, 6, 6, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 4, 4, 2, 6, 6, 27, 6, 6, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544849265 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000544849265 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544849265/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544849265/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544849265 Building ZINC000544849265 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544849265' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544849265 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000544849265 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544849265/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544849265 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 438) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/438: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](c2ccc(OC(F)F)cc2)C(F)(F)F)cc1Cl) `ZINC000544849265.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000544849265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544849265/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000544849265 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](c2ccc(OC(F)F)cc2)C(F)(F)F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 15, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 6, 6, 4, 4, 24, 27, 27, 6, 6, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 4, 4, 2, 6, 6, 27, 6, 6, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544849265 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544849265/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544849265 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 439) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/439: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](c2ccc(OC(F)F)cc2)C(F)(F)F)cc1Cl) `ZINC000544849265.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000544849265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544849265/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000544849265 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](c2ccc(OC(F)F)cc2)C(F)(F)F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 15, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 6, 6, 4, 4, 23, 27, 27, 6, 6, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 4, 4, 2, 6, 6, 27, 6, 6, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544849265 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000544849265 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544849265/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544849265/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544849265 Building ZINC000544850685 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850685' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850685 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000544850685 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850685/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850685 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 440) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/440 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/440' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(Cc1ccccc1)Cc1ccc(Br)cc1) `ZINC000544850685.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000544850685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850685/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000544850685 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(Cc1ccccc1)Cc1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 2, 2, 6, 16, 20, 20, 17, 20, 20, 6, 17, 22, 22, 19, 22, 22, 22, 3, 3, 3, 3, 3, 3, 3, 16, 16, 20, 20, 20, 20, 20, 17, 17, 22, 22, 22, 22] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850685 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850685/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850685 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 441) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/441 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/441' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(Cc1ccccc1)Cc1ccc(Br)cc1) `ZINC000544850685.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000544850685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850685/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000544850685 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(Cc1ccccc1)Cc1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 6, 13, 17, 17, 16, 17, 17, 6, 15, 19, 19, 19, 19, 19, 19, 4, 4, 4, 4, 4, 4, 4, 13, 13, 17, 17, 17, 17, 17, 15, 15, 19, 19, 19, 19] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850685 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000544850685 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850685/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850685/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850685 Building ZINC000544850685 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850685' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850685 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000544850685 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850685/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850685 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 440) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/440: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(Cc1ccccc1)Cc1ccc(Br)cc1) `ZINC000544850685.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000544850685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850685/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000544850685 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(Cc1ccccc1)Cc1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 2, 2, 6, 16, 20, 20, 17, 20, 20, 6, 17, 22, 22, 19, 22, 22, 22, 3, 3, 3, 3, 3, 3, 3, 16, 16, 20, 20, 20, 20, 20, 17, 17, 22, 22, 22, 22] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850685 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850685/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850685 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 441) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/441: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(Cc1ccccc1)Cc1ccc(Br)cc1) `ZINC000544850685.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000544850685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850685/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000544850685 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(Cc1ccccc1)Cc1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 6, 13, 17, 17, 16, 17, 17, 6, 15, 19, 19, 19, 19, 19, 19, 4, 4, 4, 4, 4, 4, 4, 13, 13, 17, 17, 17, 17, 17, 15, 15, 19, 19, 19, 19] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850685 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000544850685 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850685/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850685/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850685 Building ZINC000544850502 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850502' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850502 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000544850502 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850502/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850502 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 442) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/442 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/442' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1nc(C)c(Cc2cccc(Br)c2)s1) `ZINC000544850502.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000544850502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000544850502 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1nc(C)c(Cc2cccc(Br)c2)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 5, 1, 5, 1, 1, 1, 1, 1, 17, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 20, 50, 50, 50, 50, 50, 50, 4, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 20, 20, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 126 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850502 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850502/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850502 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 443) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/443 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/443' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1nc(C)c(Cc2cccc(Br)c2)s1) `ZINC000544850502.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000544850502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850502/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000544850502 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1nc(C)c(Cc2cccc(Br)c2)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 5, 1, 5, 1, 1, 1, 1, 1, 17, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 20, 50, 50, 50, 50, 50, 50, 4, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 20, 20, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 126 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850502 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000544850502 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850502/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850502/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850502 Building ZINC000544850502 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850502' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850502 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000544850502 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850502/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850502 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 442) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/442: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1nc(C)c(Cc2cccc(Br)c2)s1) `ZINC000544850502.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000544850502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000544850502 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1nc(C)c(Cc2cccc(Br)c2)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 5, 1, 5, 1, 1, 1, 1, 1, 17, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 20, 50, 50, 50, 50, 50, 50, 4, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 20, 20, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 126 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850502 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850502/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850502 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 443) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/443: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1nc(C)c(Cc2cccc(Br)c2)s1) `ZINC000544850502.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000544850502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850502/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000544850502 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1nc(C)c(Cc2cccc(Br)c2)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 5, 1, 5, 1, 1, 1, 1, 1, 17, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 20, 50, 50, 50, 50, 50, 50, 4, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 20, 20, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 126 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850502 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000544850502 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850502/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850502/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850502 Building ZINC000544850290 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850290' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850290 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000544850290 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850290/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850290 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 444) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/444 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/444' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](Cc2ccc(Cl)cc2)c2ccccn2)cc1Cl) `ZINC000544850290.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000544850290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850290/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000544850290 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](Cc2ccc(Cl)cc2)c2ccccn2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 16, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 6, 6, 15, 15, 15, 15, 15, 15, 15, 6, 12, 12, 12, 12, 12, 6, 6, 6, 13, 13, 13, 6, 6, 3, 15, 15, 15, 15, 15, 15, 12, 12, 12, 12, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850290 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850290/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850290 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 445) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/445 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/445' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](Cc2ccc(Cl)cc2)c2ccccn2)cc1Cl) `ZINC000544850290.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000544850290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850290/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000544850290 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](Cc2ccc(Cl)cc2)c2ccccn2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 16, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 11, 11, 11, 11, 11, 11, 11, 5, 12, 12, 12, 12, 12, 6, 6, 6, 15, 15, 15, 6, 6, 3, 11, 11, 11, 11, 11, 11, 12, 12, 12, 12, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850290 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000544850290 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850290/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850290/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850290 Building ZINC000544850290 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850290' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850290 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000544850290 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850290/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850290 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 444) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/444: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](Cc2ccc(Cl)cc2)c2ccccn2)cc1Cl) `ZINC000544850290.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000544850290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850290/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000544850290 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](Cc2ccc(Cl)cc2)c2ccccn2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 16, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 6, 6, 15, 15, 15, 15, 15, 15, 15, 6, 12, 12, 12, 12, 12, 6, 6, 6, 13, 13, 13, 6, 6, 3, 15, 15, 15, 15, 15, 15, 12, 12, 12, 12, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850290 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850290/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850290 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 445) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/445: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](Cc2ccc(Cl)cc2)c2ccccn2)cc1Cl) `ZINC000544850290.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000544850290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850290/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000544850290 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](Cc2ccc(Cl)cc2)c2ccccn2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 16, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 11, 11, 11, 11, 11, 11, 11, 5, 12, 12, 12, 12, 12, 6, 6, 6, 15, 15, 15, 6, 6, 3, 11, 11, 11, 11, 11, 11, 12, 12, 12, 12, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850290 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000544850290 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850290/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850290/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544850290 Building ZINC000544854424 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544854424' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544854424 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000544854424 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544854424/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544854424 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 446) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/446 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/446' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N(C)C2CCCCC2)c(Cl)c1) `ZINC000544854424.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000544854424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544854424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000544854424 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N(C)C2CCCCC2)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 14, 14, 14, 14, 28, 28, 48, 48, 50, 50, 50, 50, 50, 14, 14, 14, 2, 2, 2, 2, 2, 2, 2, 2, 14, 14, 48, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544854424 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544854424/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544854424 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 447) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/447 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/447' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N(C)C2CCCCC2)c(Cl)c1) `ZINC000544854424.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000544854424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544854424/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000544854424 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N(C)C2CCCCC2)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 14, 14, 14, 14, 28, 28, 48, 48, 50, 50, 50, 50, 50, 14, 14, 14, 2, 2, 2, 2, 2, 2, 2, 2, 14, 14, 48, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544854424 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000544854424 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544854424/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544854424/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544854424 Building ZINC000544854424 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544854424' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544854424 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000544854424 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544854424/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544854424 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 446) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/446: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N(C)C2CCCCC2)c(Cl)c1) `ZINC000544854424.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000544854424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544854424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000544854424 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N(C)C2CCCCC2)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 14, 14, 14, 14, 28, 28, 48, 48, 50, 50, 50, 50, 50, 14, 14, 14, 2, 2, 2, 2, 2, 2, 2, 2, 14, 14, 48, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544854424 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544854424/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544854424 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 447) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/447: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N(C)C2CCCCC2)c(Cl)c1) `ZINC000544854424.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000544854424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544854424/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000544854424 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N(C)C2CCCCC2)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 14, 14, 14, 14, 28, 28, 48, 48, 50, 50, 50, 50, 50, 14, 14, 14, 2, 2, 2, 2, 2, 2, 2, 2, 14, 14, 48, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544854424 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000544854424 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544854424/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544854424/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544854424 Building ZINC000544855458 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544855458' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544855458 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000544855458 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544855458/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544855458 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 448) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/448 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/448' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccccc2CN(C)C(=O)c2cccs2)cc1Cl) `ZINC000544855458.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000544855458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544855458/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000544855458 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccccc2CN(C)C(=O)c2cccs2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 8, 5, 1, 11, 1, 1, 1, 1, 14, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 4, 9, 15, 15, 20, 20, 28, 28, 28, 28, 2, 2, 2, 4, 4, 4, 2, 2, 1, 4, 4, 2, 4, 9, 9, 15, 15, 15, 28, 28, 28, 2] 50 rigid atoms, others: [35, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 94 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544855458 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544855458/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544855458 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 449) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/449 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/449' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2CN(C)C(=O)c2cccs2)cc1Cl) `ZINC000544855458.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000544855458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544855458/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000544855458 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2CN(C)C(=O)c2cccs2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 8, 5, 1, 11, 1, 1, 1, 1, 14, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 4, 9, 14, 14, 19, 19, 28, 28, 28, 28, 2, 2, 2, 4, 4, 4, 2, 2, 1, 4, 4, 1, 4, 9, 9, 14, 14, 14, 28, 28, 28, 2] 50 rigid atoms, others: [35, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 92 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544855458 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000544855458 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544855458/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544855458/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544855458 Building ZINC000544855458 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544855458' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544855458 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000544855458 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544855458/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544855458 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 448) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/448: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccccc2CN(C)C(=O)c2cccs2)cc1Cl) `ZINC000544855458.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000544855458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544855458/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000544855458 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccccc2CN(C)C(=O)c2cccs2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 8, 5, 1, 11, 1, 1, 1, 1, 14, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 4, 9, 15, 15, 20, 20, 28, 28, 28, 28, 2, 2, 2, 4, 4, 4, 2, 2, 1, 4, 4, 2, 4, 9, 9, 15, 15, 15, 28, 28, 28, 2] 50 rigid atoms, others: [35, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 94 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544855458 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544855458/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544855458 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 449) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/449: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2CN(C)C(=O)c2cccs2)cc1Cl) `ZINC000544855458.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000544855458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544855458/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000544855458 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2CN(C)C(=O)c2cccs2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 8, 5, 1, 11, 1, 1, 1, 1, 14, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 4, 9, 14, 14, 19, 19, 28, 28, 28, 28, 2, 2, 2, 4, 4, 4, 2, 2, 1, 4, 4, 1, 4, 9, 9, 14, 14, 14, 28, 28, 28, 2] 50 rigid atoms, others: [35, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 92 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544855458 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000544855458 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544855458/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544855458/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544855458 Building ZINC000544855109 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544855109' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544855109 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000544855109 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544855109/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544855109 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 450) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/450 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/450' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(COCc2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)c2)cc1) `ZINC000544855109.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000544855109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544855109/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000544855109 none COc1ccc(COCc2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', '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, 12, 1, 1, 1, 1, 5, 12, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 14, 29, 29, 14, 6, 6, 3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 4, 2, 2, 2, 3, 29, 29, 29, 29, 29, 29, 29, 14, 14, 6, 6, 1, 3, 3, 1, 2, 2, 4, 4, 4, 2, 3, 29, 29] 50 rigid atoms, others: [43, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544855109 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544855109/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544855109 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 451) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/451 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/451' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(COCc2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)c2)cc1) `ZINC000544855109.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000544855109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544855109/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000544855109 none COc1ccc(COCc2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', '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, 12, 1, 1, 1, 1, 5, 12, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 24, 15, 32, 32, 15, 6, 6, 3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 5, 2, 2, 2, 3, 32, 32, 32, 32, 32, 32, 32, 15, 15, 6, 6, 1, 3, 3, 1, 2, 2, 5, 5, 5, 2, 3, 32, 32] 50 rigid atoms, others: [43, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544855109 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000544855109 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544855109/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544855109/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544855109 Building ZINC000544855109 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544855109' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544855109 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000544855109 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544855109/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544855109 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 450) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/450: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(COCc2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)c2)cc1) `ZINC000544855109.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000544855109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544855109/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000544855109 none COc1ccc(COCc2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', '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, 12, 1, 1, 1, 1, 5, 12, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 14, 29, 29, 14, 6, 6, 3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 4, 2, 2, 2, 3, 29, 29, 29, 29, 29, 29, 29, 14, 14, 6, 6, 1, 3, 3, 1, 2, 2, 4, 4, 4, 2, 3, 29, 29] 50 rigid atoms, others: [43, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544855109 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544855109/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544855109 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 451) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/451: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(COCc2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)c2)cc1) `ZINC000544855109.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000544855109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544855109/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000544855109 none COc1ccc(COCc2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', '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, 12, 1, 1, 1, 1, 5, 12, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 24, 15, 32, 32, 15, 6, 6, 3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 5, 2, 2, 2, 3, 32, 32, 32, 32, 32, 32, 32, 15, 15, 6, 6, 1, 3, 3, 1, 2, 2, 5, 5, 5, 2, 3, 32, 32] 50 rigid atoms, others: [43, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544855109 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000544855109 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544855109/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544855109/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544855109 Building ZINC000544856710 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544856710' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544856710 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000544856710 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544856710/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544856710 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 452) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/452 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/452' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(Cl)ccc2c2nc(C3CC3)no2)cc1Cl) `ZINC000544856710.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000544856710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544856710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000544856710 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(Cl)ccc2c2nc(C3CC3)no2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 16, 1, 1, 1, 1, 8, 1, 5, 5, 5, 8, 12, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 3, 6, 6, 6, 17, 17, 17, 33, 33, 17, 17, 4, 4, 4, 9, 9, 9, 4, 4, 3, 6, 6, 6, 33, 33, 33, 33, 33, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544856710 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544856710/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544856710 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 453) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/453 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/453' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(Cl)ccc2c2nc(C3CC3)no2)cc1Cl) `ZINC000544856710.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000544856710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544856710/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000544856710 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(Cl)ccc2c2nc(C3CC3)no2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 16, 1, 1, 1, 1, 8, 1, 5, 5, 5, 8, 12, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 4, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 3, 6, 6, 6, 15, 15, 15, 32, 32, 15, 15, 4, 4, 4, 9, 9, 9, 4, 4, 3, 6, 6, 6, 32, 32, 32, 32, 32, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544856710 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000544856710 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544856710/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544856710/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544856710 Building ZINC000544856710 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544856710' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544856710 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000544856710 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544856710/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544856710 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 452) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/452: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(Cl)ccc2c2nc(C3CC3)no2)cc1Cl) `ZINC000544856710.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000544856710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544856710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000544856710 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(Cl)ccc2c2nc(C3CC3)no2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 16, 1, 1, 1, 1, 8, 1, 5, 5, 5, 8, 12, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 3, 6, 6, 6, 17, 17, 17, 33, 33, 17, 17, 4, 4, 4, 9, 9, 9, 4, 4, 3, 6, 6, 6, 33, 33, 33, 33, 33, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544856710 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544856710/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544856710 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 453) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/453: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(Cl)ccc2c2nc(C3CC3)no2)cc1Cl) `ZINC000544856710.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000544856710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544856710/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000544856710 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(Cl)ccc2c2nc(C3CC3)no2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 16, 1, 1, 1, 1, 8, 1, 5, 5, 5, 8, 12, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 4, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 3, 6, 6, 6, 15, 15, 15, 32, 32, 15, 15, 4, 4, 4, 9, 9, 9, 4, 4, 3, 6, 6, 6, 32, 32, 32, 32, 32, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544856710 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000544856710 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544856710/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544856710/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544856710 Building ZINC000544872394 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544872394' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544872394 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000544872394 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544872394/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544872394 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 454) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/454 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/454' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Oc3nncc4ccccc43)cc2)cc1Cl) `ZINC000544872394.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000544872394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544872394/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000544872394 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Oc3nncc4ccccc43)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 14, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 4, 4, 4, 4, 6, 6, 6, 4, 4, 2, 4, 4, 27, 27, 27, 27, 27, 4, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544872394 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544872394/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544872394 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 455) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/455 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/455' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(Oc3nncc4ccccc43)cc2)cc1Cl) `ZINC000544872394.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000544872394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544872394/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000544872394 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(Oc3nncc4ccccc43)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 3, 4, 14, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 4, 4, 4, 4, 6, 6, 6, 4, 4, 2, 4, 4, 27, 27, 27, 27, 27, 4, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544872394 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000544872394 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544872394/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544872394/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544872394 Building ZINC000544872394 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544872394' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544872394 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000544872394 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544872394/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544872394 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 454) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/454: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Oc3nncc4ccccc43)cc2)cc1Cl) `ZINC000544872394.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000544872394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544872394/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000544872394 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Oc3nncc4ccccc43)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 14, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 4, 4, 4, 4, 6, 6, 6, 4, 4, 2, 4, 4, 27, 27, 27, 27, 27, 4, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544872394 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544872394/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544872394 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 455) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/455: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(Oc3nncc4ccccc43)cc2)cc1Cl) `ZINC000544872394.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000544872394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544872394/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000544872394 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(Oc3nncc4ccccc43)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 3, 4, 14, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 4, 4, 4, 4, 6, 6, 6, 4, 4, 2, 4, 4, 27, 27, 27, 27, 27, 4, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544872394 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000544872394 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544872394/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544872394/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000544872394 Building ZINC000468186515 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000468186515' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000468186515 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000468186515 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000468186515/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000468186515 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 456) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/456 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/456' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCc1ccccc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000468186515.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000468186515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000468186515/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000468186515 none COCCc1ccccc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 11, 11, 11, 9, 9, 6, 6, 3, 3, 3, 3, 1, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2] 50 rigid atoms, others: [43, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000468186515 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000468186515/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000468186515 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 457) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/457 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/457' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000468186515.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000468186515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000468186515/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000468186515 none COCCc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 11, 11, 11, 9, 9, 6, 6, 3, 3, 3, 3, 1, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2] 50 rigid atoms, others: [43, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000468186515 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000468186515 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000468186515/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000468186515/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000468186515 Building ZINC000468186515 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000468186515' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000468186515 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000468186515 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000468186515/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000468186515 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 456) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/456: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCc1ccccc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000468186515.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000468186515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000468186515/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000468186515 none COCCc1ccccc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 11, 11, 11, 9, 9, 6, 6, 3, 3, 3, 3, 1, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2] 50 rigid atoms, others: [43, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000468186515 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000468186515/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000468186515 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 457) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/457: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000468186515.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000468186515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000468186515/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000468186515 none COCCc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 11, 11, 11, 9, 9, 6, 6, 3, 3, 3, 3, 1, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2] 50 rigid atoms, others: [43, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000468186515 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000468186515 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000468186515/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000468186515/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000468186515 Building ZINC000545446856 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545446856' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545446856 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000545446856 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545446856/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545446856 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 458) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/458 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/458' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2cc(Br)ccc2F)C2CC2)cc1Cl) `ZINC000545446856.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000545446856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545446856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000545446856 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2cc(Br)ccc2F)C2CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 17, 1, 1, 1, 15, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 5, 9, 18, 18, 18, 13, 18, 18, 18, 5, 6, 6, 4, 4, 4, 6, 6, 6, 4, 4, 9, 9, 18, 13, 18, 6, 6, 6, 6, 6, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 87 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545446856 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545446856/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545446856 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 459) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/459 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/459' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2cc(Br)ccc2F)C2CC2)cc1Cl) `ZINC000545446856.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000545446856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545446856/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000545446856 none COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2cc(Br)ccc2F)C2CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 17, 1, 1, 1, 15, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 2, 2, 4, 8, 16, 16, 16, 10, 16, 16, 16, 4, 7, 7, 6, 6, 6, 12, 12, 12, 6, 6, 8, 8, 16, 10, 16, 7, 7, 7, 7, 7, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 102 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545446856 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000545446856 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545446856/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545446856/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545446856 Building ZINC000545446856 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545446856' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545446856 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000545446856 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545446856/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545446856 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 458) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/458: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2cc(Br)ccc2F)C2CC2)cc1Cl) `ZINC000545446856.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000545446856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545446856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000545446856 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2cc(Br)ccc2F)C2CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 17, 1, 1, 1, 15, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 5, 9, 18, 18, 18, 13, 18, 18, 18, 5, 6, 6, 4, 4, 4, 6, 6, 6, 4, 4, 9, 9, 18, 13, 18, 6, 6, 6, 6, 6, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 87 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545446856 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545446856/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545446856 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 459) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/459: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2cc(Br)ccc2F)C2CC2)cc1Cl) `ZINC000545446856.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000545446856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545446856/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000545446856 none COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2cc(Br)ccc2F)C2CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 17, 1, 1, 1, 15, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 2, 2, 4, 8, 16, 16, 16, 10, 16, 16, 16, 4, 7, 7, 6, 6, 6, 12, 12, 12, 6, 6, 8, 8, 16, 10, 16, 7, 7, 7, 7, 7, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 102 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545446856 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000545446856 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545446856/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545446856/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545446856 Building ZINC000545447445 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545447445' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545447445 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000545447445 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545447445/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545447445 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 460) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/460 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/460' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2cccs2)c2ccc3c(c2)OCCO3)cc1Cl) `ZINC000545447445.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000545447445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545447445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000545447445 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2cccs2)c2ccc3c(c2)OCCO3)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 2, 5, 5, 1, 1, 1, 1, 2, 2, 2, 5, 8, 8, 8, 8, 2, 8, 12, 12, 12, 8, 12, 12, 12, 12, 5, 5, 5, 10, 10, 10, 5, 5, 5, 5, 8, 8, 8, 12, 12, 12, 12, 12, 12, 12, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545447445 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545447445/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545447445 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 461) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/461 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/461' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2cccs2)c2ccc3c(c2)OCCO3)cc1Cl) `ZINC000545447445.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000545447445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545447445/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000545447445 none COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2cccs2)c2ccc3c(c2)OCCO3)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 2, 5, 5, 1, 1, 1, 1, 2, 2, 2, 5, 8, 8, 8, 8, 2, 8, 12, 12, 12, 8, 12, 12, 12, 12, 5, 5, 5, 10, 10, 10, 5, 5, 5, 5, 8, 8, 8, 12, 12, 12, 12, 12, 12, 12, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545447445 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000545447445 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545447445/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545447445/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545447445 Building ZINC000545447445 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545447445' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545447445 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000545447445 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545447445/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545447445 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 460) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/460: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2cccs2)c2ccc3c(c2)OCCO3)cc1Cl) `ZINC000545447445.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000545447445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545447445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000545447445 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2cccs2)c2ccc3c(c2)OCCO3)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 2, 5, 5, 1, 1, 1, 1, 2, 2, 2, 5, 8, 8, 8, 8, 2, 8, 12, 12, 12, 8, 12, 12, 12, 12, 5, 5, 5, 10, 10, 10, 5, 5, 5, 5, 8, 8, 8, 12, 12, 12, 12, 12, 12, 12, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545447445 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545447445/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545447445 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 461) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/461: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2cccs2)c2ccc3c(c2)OCCO3)cc1Cl) `ZINC000545447445.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000545447445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545447445/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000545447445 none COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2cccs2)c2ccc3c(c2)OCCO3)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 2, 5, 5, 1, 1, 1, 1, 2, 2, 2, 5, 8, 8, 8, 8, 2, 8, 12, 12, 12, 8, 12, 12, 12, 12, 5, 5, 5, 10, 10, 10, 5, 5, 5, 5, 8, 8, 8, 12, 12, 12, 12, 12, 12, 12, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545447445 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000545447445 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545447445/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545447445/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545447445 Building ZINC000545447505 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545447505' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545447505 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000545447505 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545447505/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545447505 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 462) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/462 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/462' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(Cc1ccc(OCc2cccs2)c(OC)c1)C(=O)[C@@]([O-])([SiH3])c1ccccc1OC) `ZINC000545447505.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000545447505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545447505/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000545447505 none CCN(Cc1ccc(OCc2cccs2)c(OC)c1)C(=O)[C@@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 14, 1, 12, 5, 1, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 3, 11, 18, 37, 37, 37, 37, 3, 3, 7, 3, 1, 1, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 18, 18, 37, 37, 37, 7, 7, 7, 3, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 35, 4, 33, 19, 32, 34, 3, 20, 21, 22, 23, 36, 37, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545447505 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545447505/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545447505 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 463) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/463 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/463' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(Cc1ccc(OCc2cccs2)c(OC)c1)C(=O)[C@]([O-])([SiH3])c1ccccc1OC) `ZINC000545447505.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000545447505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545447505/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000545447505 none CCN(Cc1ccc(OCc2cccs2)c(OC)c1)C(=O)[C@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 14, 1, 12, 5, 1, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 4, 14, 20, 41, 41, 41, 41, 4, 4, 9, 4, 1, 1, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 20, 20, 41, 41, 41, 9, 9, 9, 4, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 35, 4, 33, 19, 32, 34, 3, 20, 21, 22, 23, 36, 37, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545447505 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000545447505 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545447505/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545447505/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545447505 Building ZINC000545447505 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545447505' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545447505 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000545447505 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545447505/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545447505 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 462) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/462: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(Cc1ccc(OCc2cccs2)c(OC)c1)C(=O)[C@@]([O-])([SiH3])c1ccccc1OC) `ZINC000545447505.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000545447505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545447505/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000545447505 none CCN(Cc1ccc(OCc2cccs2)c(OC)c1)C(=O)[C@@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 14, 1, 12, 5, 1, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 3, 11, 18, 37, 37, 37, 37, 3, 3, 7, 3, 1, 1, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 18, 18, 37, 37, 37, 7, 7, 7, 3, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 35, 4, 33, 19, 32, 34, 3, 20, 21, 22, 23, 36, 37, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545447505 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545447505/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545447505 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 463) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/463: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(Cc1ccc(OCc2cccs2)c(OC)c1)C(=O)[C@]([O-])([SiH3])c1ccccc1OC) `ZINC000545447505.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000545447505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545447505/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000545447505 none CCN(Cc1ccc(OCc2cccs2)c(OC)c1)C(=O)[C@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 14, 1, 12, 5, 1, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 4, 14, 20, 41, 41, 41, 41, 4, 4, 9, 4, 1, 1, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 20, 20, 41, 41, 41, 9, 9, 9, 4, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 35, 4, 33, 19, 32, 34, 3, 20, 21, 22, 23, 36, 37, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545447505 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000545447505 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545447505/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545447505/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545447505 Building ZINC000545448499 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545448499' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545448499 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000545448499 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545448499/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545448499 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 464) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/464 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/464' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1nc2cc(C(F)(F)F)ccc2n1Cc1ccco1) `ZINC000545448499.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000545448499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545448499/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000545448499 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1nc2cc(C(F)(F)F)ccc2n1Cc1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 3, 5, 5, 1, 1, 1, 1, 5, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 27, 42, 42, 42, 42, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 27, 27, 42, 42, 42] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545448499 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545448499/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545448499 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 465) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/465 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/465' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1nc2cc(C(F)(F)F)ccc2n1Cc1ccco1) `ZINC000545448499.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000545448499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545448499/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000545448499 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1nc2cc(C(F)(F)F)ccc2n1Cc1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 3, 5, 5, 1, 1, 1, 1, 5, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 28, 43, 43, 43, 43, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 28, 28, 43, 43, 43] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545448499 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000545448499 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545448499/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545448499/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545448499 Building ZINC000545448499 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545448499' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545448499 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000545448499 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545448499/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545448499 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 464) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/464: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1nc2cc(C(F)(F)F)ccc2n1Cc1ccco1) `ZINC000545448499.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000545448499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545448499/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000545448499 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1nc2cc(C(F)(F)F)ccc2n1Cc1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 3, 5, 5, 1, 1, 1, 1, 5, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 27, 42, 42, 42, 42, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 27, 27, 42, 42, 42] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545448499 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545448499/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545448499 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 465) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/465: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1nc2cc(C(F)(F)F)ccc2n1Cc1ccco1) `ZINC000545448499.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000545448499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545448499/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000545448499 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1nc2cc(C(F)(F)F)ccc2n1Cc1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 3, 5, 5, 1, 1, 1, 1, 5, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 28, 43, 43, 43, 43, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 28, 28, 43, 43, 43] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545448499 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000545448499 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545448499/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545448499/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545448499 Building ZINC000545452865 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545452865' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545452865 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000545452865 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545452865/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545452865 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 466) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/466 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/466' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(Oc3ccc(C)cc3OC)nc2)cc1Cl) `ZINC000545452865.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000545452865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545452865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000545452865 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(Oc3ccc(C)cc3OC)nc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 1, 1, 12, 5, 8, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 20, 29, 29, 26, 29, 29, 29, 29, 29, 6, 6, 4, 4, 4, 7, 7, 7, 4, 4, 2, 6, 6, 29, 29, 29, 29, 29, 29, 29, 29, 29, 6, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545452865 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545452865/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545452865 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 467) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/467 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/467' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Oc3ccc(C)cc3OC)nc2)cc1Cl) `ZINC000545452865.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000545452865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545452865/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000545452865 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Oc3ccc(C)cc3OC)nc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 1, 1, 12, 5, 8, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 20, 29, 29, 26, 29, 29, 29, 29, 29, 6, 6, 4, 4, 4, 7, 7, 7, 4, 4, 2, 6, 6, 29, 29, 29, 29, 29, 29, 29, 29, 29, 6, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545452865 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000545452865 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545452865/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545452865/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545452865 Building ZINC000545452865 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545452865' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545452865 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000545452865 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545452865/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545452865 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 466) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/466: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(Oc3ccc(C)cc3OC)nc2)cc1Cl) `ZINC000545452865.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000545452865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545452865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000545452865 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(Oc3ccc(C)cc3OC)nc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 1, 1, 12, 5, 8, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 20, 29, 29, 26, 29, 29, 29, 29, 29, 6, 6, 4, 4, 4, 7, 7, 7, 4, 4, 2, 6, 6, 29, 29, 29, 29, 29, 29, 29, 29, 29, 6, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545452865 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545452865/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545452865 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 467) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/467: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Oc3ccc(C)cc3OC)nc2)cc1Cl) `ZINC000545452865.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000545452865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545452865/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000545452865 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Oc3ccc(C)cc3OC)nc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 1, 1, 12, 5, 8, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 20, 29, 29, 26, 29, 29, 29, 29, 29, 6, 6, 4, 4, 4, 7, 7, 7, 4, 4, 2, 6, 6, 29, 29, 29, 29, 29, 29, 29, 29, 29, 6, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545452865 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000545452865 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545452865/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545452865/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545452865 Building ZINC000545457118 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545457118' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545457118 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000545457118 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545457118/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545457118 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 468) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/468 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/468' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(OCc3ccccn3)c(Cl)c2)cc1Cl) `ZINC000545457118.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000545457118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545457118/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000545457118 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(OCc3ccccn3)c(Cl)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 8, 1, 16, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 20, 24, 28, 28, 28, 28, 28, 4, 4, 4, 2, 2, 2, 4, 4, 4, 2, 2, 1, 4, 4, 24, 24, 28, 28, 28, 28, 4, 2] 50 rigid atoms, others: [34, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545457118 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545457118/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545457118 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 469) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/469 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/469' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(OCc3ccccn3)c(Cl)c2)cc1Cl) `ZINC000545457118.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000545457118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545457118/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000545457118 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(OCc3ccccn3)c(Cl)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 8, 1, 16, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 20, 24, 28, 28, 28, 28, 28, 4, 4, 4, 2, 2, 2, 4, 4, 4, 2, 2, 1, 4, 4, 24, 24, 28, 28, 28, 28, 4, 2] 50 rigid atoms, others: [34, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545457118 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000545457118 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545457118/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545457118/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545457118 Building ZINC000545457118 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545457118' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545457118 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000545457118 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545457118/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545457118 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 468) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/468: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(OCc3ccccn3)c(Cl)c2)cc1Cl) `ZINC000545457118.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000545457118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545457118/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000545457118 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(OCc3ccccn3)c(Cl)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 8, 1, 16, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 20, 24, 28, 28, 28, 28, 28, 4, 4, 4, 2, 2, 2, 4, 4, 4, 2, 2, 1, 4, 4, 24, 24, 28, 28, 28, 28, 4, 2] 50 rigid atoms, others: [34, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545457118 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545457118/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545457118 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 469) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/469: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(OCc3ccccn3)c(Cl)c2)cc1Cl) `ZINC000545457118.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000545457118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545457118/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000545457118 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(OCc3ccccn3)c(Cl)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 8, 1, 16, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 20, 24, 28, 28, 28, 28, 28, 4, 4, 4, 2, 2, 2, 4, 4, 4, 2, 2, 1, 4, 4, 24, 24, 28, 28, 28, 28, 4, 2] 50 rigid atoms, others: [34, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545457118 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000545457118 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545457118/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545457118/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545457118 Building ZINC000545458891 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545458891' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545458891 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000545458891 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545458891/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545458891 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 470) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/470 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/470' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H](C)c1nc(c2ccc(Br)cc2)cs1) `ZINC000545458891.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000545458891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545458891/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000545458891 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H](C)c1nc(c2ccc(Br)cc2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 31, 31, 31, 50, 50, 31, 31, 50, 50, 31, 31, 2, 2, 2, 2, 2, 2, 2, 3, 5, 5, 5, 50, 50, 50, 50, 31] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545458891 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545458891/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545458891 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 471) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/471 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/471' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H](C)c1nc(c2ccc(Br)cc2)cs1) `ZINC000545458891.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000545458891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545458891/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000545458891 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H](C)c1nc(c2ccc(Br)cc2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 22, 22, 22, 50, 50, 22, 36, 50, 50, 22, 22, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 50, 50, 50, 50, 22] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545458891 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000545458891 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545458891/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545458891/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545458891 Building ZINC000545458891 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545458891' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545458891 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000545458891 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545458891/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545458891 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 470) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/470: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H](C)c1nc(c2ccc(Br)cc2)cs1) `ZINC000545458891.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000545458891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545458891/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000545458891 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H](C)c1nc(c2ccc(Br)cc2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 31, 31, 31, 50, 50, 31, 31, 50, 50, 31, 31, 2, 2, 2, 2, 2, 2, 2, 3, 5, 5, 5, 50, 50, 50, 50, 31] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545458891 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545458891/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545458891 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 471) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/471: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H](C)c1nc(c2ccc(Br)cc2)cs1) `ZINC000545458891.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000545458891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545458891/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000545458891 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H](C)c1nc(c2ccc(Br)cc2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 22, 22, 22, 50, 50, 22, 36, 50, 50, 22, 22, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 50, 50, 50, 50, 22] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545458891 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000545458891 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545458891/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545458891/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545458891 Building ZINC000545458892 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545458892' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545458892 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000545458892 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545458892/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545458892 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 472) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/472 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/472' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H](C)c1nc(c2ccc(Br)cc2)cs1) `ZINC000545458892.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000545458892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545458892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000545458892 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H](C)c1nc(c2ccc(Br)cc2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 23, 23, 23, 50, 50, 23, 34, 50, 50, 23, 23, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 50, 50, 50, 50, 23] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545458892 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545458892/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545458892 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 473) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/473 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/473' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)c1nc(c2ccc(Br)cc2)cs1) `ZINC000545458892.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000545458892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545458892/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000545458892 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)c1nc(c2ccc(Br)cc2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 31, 31, 31, 50, 50, 31, 49, 50, 50, 31, 31, 2, 2, 2, 2, 2, 2, 2, 3, 5, 5, 5, 50, 50, 50, 50, 31] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545458892 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000545458892 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545458892/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545458892/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545458892 Building ZINC000545458892 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545458892' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545458892 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000545458892 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545458892/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545458892 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 472) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/472: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H](C)c1nc(c2ccc(Br)cc2)cs1) `ZINC000545458892.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000545458892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545458892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000545458892 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H](C)c1nc(c2ccc(Br)cc2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 23, 23, 23, 50, 50, 23, 34, 50, 50, 23, 23, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 50, 50, 50, 50, 23] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545458892 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545458892/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545458892 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 473) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/473: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)c1nc(c2ccc(Br)cc2)cs1) `ZINC000545458892.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000545458892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545458892/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000545458892 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)c1nc(c2ccc(Br)cc2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 31, 31, 31, 50, 50, 31, 49, 50, 50, 31, 31, 2, 2, 2, 2, 2, 2, 2, 3, 5, 5, 5, 50, 50, 50, 50, 31] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545458892 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000545458892 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545458892/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545458892/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545458892 Building ZINC000545460304 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545460304' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545460304 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000545460304 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545460304/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545460304 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 474) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/474 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/474' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2CCc2ccc(OC)c(OC)c2)cc1Cl) `ZINC000545460304.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000545460304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545460304/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000545460304 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2CCc2ccc(OC)c(OC)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 5, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 2, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 6, 6, 12, 12, 12, 12, 26, 12, 12, 26, 12, 2, 2, 2, 6, 6, 6, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 12, 12, 26, 26, 26, 26, 26, 26, 12, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 89 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545460304 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545460304/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545460304 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 475) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/475 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/475' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2CCc2ccc(OC)c(OC)c2)cc1Cl) `ZINC000545460304.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000545460304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545460304/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000545460304 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2CCc2ccc(OC)c(OC)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 5, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 20, 10, 10, 25, 10, 2, 2, 2, 4, 4, 4, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 20, 20, 20, 25, 25, 25, 10, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545460304 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000545460304 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545460304/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545460304/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545460304 Building ZINC000545460304 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545460304' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545460304 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000545460304 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545460304/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545460304 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 474) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/474: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2CCc2ccc(OC)c(OC)c2)cc1Cl) `ZINC000545460304.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000545460304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545460304/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000545460304 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2CCc2ccc(OC)c(OC)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 5, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 2, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 6, 6, 12, 12, 12, 12, 26, 12, 12, 26, 12, 2, 2, 2, 6, 6, 6, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 12, 12, 26, 26, 26, 26, 26, 26, 12, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 89 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545460304 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545460304/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545460304 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 475) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/475: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2CCc2ccc(OC)c(OC)c2)cc1Cl) `ZINC000545460304.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000545460304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545460304/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000545460304 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2CCc2ccc(OC)c(OC)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 5, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 20, 10, 10, 25, 10, 2, 2, 2, 4, 4, 4, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 20, 20, 20, 25, 25, 25, 10, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545460304 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000545460304 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545460304/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545460304/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545460304 Building ZINC000545460305 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545460305' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545460305 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000545460305 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545460305/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545460305 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 476) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/476 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/476' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCC[C@H]2CCc2ccc(OC)c(OC)c2)cc1Cl) `ZINC000545460305.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000545460305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545460305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000545460305 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCC[C@H]2CCc2ccc(OC)c(OC)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 5, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 5, 5, 5, 6, 6, 11, 11, 11, 11, 23, 11, 11, 25, 11, 2, 2, 2, 4, 4, 4, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 11, 11, 23, 23, 23, 25, 25, 25, 11, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545460305 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545460305/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545460305 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 477) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/477 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/477' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@H]2CCc2ccc(OC)c(OC)c2)cc1Cl) `ZINC000545460305.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000545460305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545460305/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000545460305 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@H]2CCc2ccc(OC)c(OC)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 5, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 2, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 6, 6, 13, 13, 13, 13, 27, 13, 13, 24, 13, 2, 2, 2, 6, 6, 6, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 13, 13, 27, 27, 27, 24, 24, 24, 13, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 84 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545460305 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000545460305 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545460305/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545460305/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545460305 Building ZINC000545460305 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545460305' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545460305 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000545460305 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545460305/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545460305 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 476) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/476: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCC[C@H]2CCc2ccc(OC)c(OC)c2)cc1Cl) `ZINC000545460305.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000545460305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545460305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000545460305 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCC[C@H]2CCc2ccc(OC)c(OC)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 5, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 5, 5, 5, 6, 6, 11, 11, 11, 11, 23, 11, 11, 25, 11, 2, 2, 2, 4, 4, 4, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 11, 11, 23, 23, 23, 25, 25, 25, 11, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545460305 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545460305/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545460305 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 477) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/477: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@H]2CCc2ccc(OC)c(OC)c2)cc1Cl) `ZINC000545460305.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000545460305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545460305/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000545460305 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@H]2CCc2ccc(OC)c(OC)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 5, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 2, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 6, 6, 13, 13, 13, 13, 27, 13, 13, 24, 13, 2, 2, 2, 6, 6, 6, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 13, 13, 27, 27, 27, 24, 24, 24, 13, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 84 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545460305 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000545460305 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545460305/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545460305/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545460305 Building ZINC000545480406 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545480406' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545480406 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000545480406 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545480406/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545480406 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 478) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/478 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/478' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(NC(=O)c3ccco3)c(Cl)c2)cc1Cl) `ZINC000545480406.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000545480406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545480406/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000545480406 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(NC(=O)c3ccco3)c(Cl)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 12, 1, 16, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 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] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 2, 12, 12, 8, 12, 20, 20, 20, 20, 20, 20, 20, 12, 12, 12, 5, 5, 5, 9, 9, 9, 5, 5, 2, 12, 12, 20, 20, 20, 20, 12, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545480406 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545480406/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545480406 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 479) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/479 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/479' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(NC(=O)c3ccco3)c(Cl)c2)cc1Cl) `ZINC000545480406.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000545480406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545480406/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000545480406 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(NC(=O)c3ccco3)c(Cl)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 12, 1, 16, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 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] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 2, 12, 12, 8, 12, 21, 21, 21, 21, 21, 21, 21, 12, 12, 12, 5, 5, 5, 9, 9, 9, 5, 5, 2, 12, 12, 21, 21, 21, 21, 12, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545480406 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000545480406 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545480406/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545480406/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545480406 Building ZINC000545480406 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545480406' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545480406 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000545480406 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545480406/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545480406 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 478) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/478: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(NC(=O)c3ccco3)c(Cl)c2)cc1Cl) `ZINC000545480406.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000545480406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545480406/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000545480406 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(NC(=O)c3ccco3)c(Cl)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 12, 1, 16, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 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] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 2, 12, 12, 8, 12, 20, 20, 20, 20, 20, 20, 20, 12, 12, 12, 5, 5, 5, 9, 9, 9, 5, 5, 2, 12, 12, 20, 20, 20, 20, 12, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545480406 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545480406/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545480406 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 479) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/479: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(NC(=O)c3ccco3)c(Cl)c2)cc1Cl) `ZINC000545480406.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000545480406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545480406/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000545480406 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(NC(=O)c3ccco3)c(Cl)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 12, 1, 16, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 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] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 2, 12, 12, 8, 12, 21, 21, 21, 21, 21, 21, 21, 12, 12, 12, 5, 5, 5, 9, 9, 9, 5, 5, 2, 12, 12, 21, 21, 21, 21, 12, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545480406 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000545480406 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545480406/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545480406/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545480406 Building ZINC000545479908 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545479908' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545479908 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000545479908 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545479908/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545479908 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 480) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/480 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/480' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ccccc1CN(C)C(=O)c1cc2ccccc2o1) `ZINC000545479908.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000545479908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545479908/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000545479908 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ccccc1CN(C)C(=O)c1cc2ccccc2o1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 8, 22, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 3, 8, 8, 8, 8, 22, 22, 34, 34, 34, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 173 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545479908 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545479908/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545479908 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 481) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/481 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/481' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1CN(C)C(=O)c1cc2ccccc2o1) `ZINC000545479908.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000545479908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545479908/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000545479908 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1CN(C)C(=O)c1cc2ccccc2o1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 8, 8, 3, 8, 8, 8, 23, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 3, 8, 8, 3, 8, 23, 23, 35, 35, 35, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 184 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545479908 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000545479908 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545479908/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545479908/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545479908 Building ZINC000545479908 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545479908' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545479908 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000545479908 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545479908/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545479908 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 480) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/480: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ccccc1CN(C)C(=O)c1cc2ccccc2o1) `ZINC000545479908.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000545479908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545479908/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000545479908 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ccccc1CN(C)C(=O)c1cc2ccccc2o1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 8, 22, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 3, 8, 8, 8, 8, 22, 22, 34, 34, 34, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 173 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545479908 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545479908/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545479908 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 481) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/481: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1CN(C)C(=O)c1cc2ccccc2o1) `ZINC000545479908.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000545479908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545479908/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000545479908 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1CN(C)C(=O)c1cc2ccccc2o1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 8, 8, 3, 8, 8, 8, 23, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 3, 8, 8, 3, 8, 23, 23, 35, 35, 35, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 184 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545479908 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000545479908 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545479908/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545479908/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545479908 Building ZINC000545480882 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545480882' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545480882 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000545480882 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545480882/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545480882 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 482) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/482 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/482' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)CCC(=O)N2Cc1ccc(Cl)cc1) `ZINC000545480882.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000545480882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545480882/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000545480882 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)CCC(=O)N2Cc1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 12, 22, 22, 22, 12, 22, 22, 22, 22, 14, 22, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 22, 22, 22, 22, 22, 22, 22, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 250 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545480882 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545480882/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545480882 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 483) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/483 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/483' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)CCC(=O)N2Cc1ccc(Cl)cc1) `ZINC000545480882.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000545480882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545480882/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000545480882 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)CCC(=O)N2Cc1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 12, 22, 22, 22, 12, 22, 22, 22, 22, 15, 22, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 22, 22, 22, 22, 22, 22, 22, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 247 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545480882 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000545480882 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545480882/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545480882/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545480882 Building ZINC000545480882 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545480882' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545480882 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000545480882 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545480882/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545480882 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 482) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/482: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)CCC(=O)N2Cc1ccc(Cl)cc1) `ZINC000545480882.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000545480882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545480882/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000545480882 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)CCC(=O)N2Cc1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 12, 22, 22, 22, 12, 22, 22, 22, 22, 14, 22, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 22, 22, 22, 22, 22, 22, 22, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 250 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545480882 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545480882/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545480882 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 483) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/483: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)CCC(=O)N2Cc1ccc(Cl)cc1) `ZINC000545480882.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000545480882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545480882/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000545480882 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)CCC(=O)N2Cc1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 12, 22, 22, 22, 12, 22, 22, 22, 22, 15, 22, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 22, 22, 22, 22, 22, 22, 22, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 247 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545480882 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000545480882 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545480882/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545480882/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545480882 Building ZINC000545485365 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545485365' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545485365 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000545485365 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545485365/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545485365 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 484) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/484 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/484' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(NC(=O)N3CCCCCC3)cc2)cc1Cl) `ZINC000545485365.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000545485365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545485365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000545485365 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(NC(=O)N3CCCCCC3)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 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] 0 hydrogens 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, 3, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 2, 10, 19, 28, 28, 28, 28, 28, 28, 28, 4, 4, 4, 4, 4, 10, 10, 10, 4, 4, 2, 4, 4, 10, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 4, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 93 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545485365 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545485365/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545485365 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 485) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/485 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/485' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(NC(=O)N3CCCCCC3)cc2)cc1Cl) `ZINC000545485365.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000545485365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545485365/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000545485365 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(NC(=O)N3CCCCCC3)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 2, 12, 21, 28, 28, 28, 28, 28, 28, 28, 4, 4, 4, 4, 4, 10, 10, 10, 4, 4, 2, 4, 4, 12, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 4, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 90 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545485365 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000545485365 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545485365/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545485365/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545485365 Building ZINC000545485365 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545485365' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545485365 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000545485365 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545485365/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545485365 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 484) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/484: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(NC(=O)N3CCCCCC3)cc2)cc1Cl) `ZINC000545485365.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000545485365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545485365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000545485365 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(NC(=O)N3CCCCCC3)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 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] 0 hydrogens 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, 3, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 2, 10, 19, 28, 28, 28, 28, 28, 28, 28, 4, 4, 4, 4, 4, 10, 10, 10, 4, 4, 2, 4, 4, 10, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 4, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 93 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545485365 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545485365/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545485365 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 485) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/485: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(NC(=O)N3CCCCCC3)cc2)cc1Cl) `ZINC000545485365.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000545485365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545485365/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000545485365 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(NC(=O)N3CCCCCC3)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 2, 12, 21, 28, 28, 28, 28, 28, 28, 28, 4, 4, 4, 4, 4, 10, 10, 10, 4, 4, 2, 4, 4, 12, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 4, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 90 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545485365 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000545485365 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545485365/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545485365/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545485365 Building ZINC000545487615 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545487615' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545487615 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000545487615 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545487615/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545487615 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 486) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/486 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/486' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](c3nc4ccccc4n3C(C)C)C2)cc1Cl) `ZINC000545487615.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000545487615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545487615/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000545487615 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](c3nc4ccccc4n3C(C)C)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 1, 4, 6, 10, 10, 10, 10, 10, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 6, 6, 6, 14, 14, 14, 6, 6, 10, 10, 10, 10, 10, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 10, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 69 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545487615 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545487615/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545487615 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 487) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/487 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/487' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](c3nc4ccccc4n3C(C)C)C2)cc1Cl) `ZINC000545487615.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000545487615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545487615/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000545487615 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](c3nc4ccccc4n3C(C)C)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 5, 8, 11, 11, 11, 11, 11, 11, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 11, 6, 6, 6, 11, 11, 11, 6, 6, 11, 11, 11, 11, 11, 11, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 11, 11, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 69 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545487615 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000545487615 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545487615/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545487615/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545487615 Building ZINC000545487615 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545487615' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545487615 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000545487615 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545487615/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545487615 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 486) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/486: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](c3nc4ccccc4n3C(C)C)C2)cc1Cl) `ZINC000545487615.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000545487615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545487615/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000545487615 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](c3nc4ccccc4n3C(C)C)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 1, 4, 6, 10, 10, 10, 10, 10, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 6, 6, 6, 14, 14, 14, 6, 6, 10, 10, 10, 10, 10, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 10, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 69 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545487615 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545487615/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545487615 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 487) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/487: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](c3nc4ccccc4n3C(C)C)C2)cc1Cl) `ZINC000545487615.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000545487615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545487615/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000545487615 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](c3nc4ccccc4n3C(C)C)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 5, 8, 11, 11, 11, 11, 11, 11, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 11, 6, 6, 6, 11, 11, 11, 6, 6, 11, 11, 11, 11, 11, 11, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 11, 11, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 69 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545487615 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000545487615 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545487615/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545487615/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545487615 Building ZINC000545487620 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545487620' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545487620 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000545487620 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545487620/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545487620 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 488) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/488 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/488' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](c3nc4ccccc4n3C(C)C)C2)cc1Cl) `ZINC000545487620.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000545487620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545487620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000545487620 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](c3nc4ccccc4n3C(C)C)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 2, 5, 7, 10, 10, 10, 10, 10, 10, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 10, 6, 6, 6, 12, 12, 12, 6, 6, 10, 10, 10, 10, 10, 10, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 10, 10, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 73 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545487620 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545487620/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545487620 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 489) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/489 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/489' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](c3nc4ccccc4n3C(C)C)C2)cc1Cl) `ZINC000545487620.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000545487620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545487620/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000545487620 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](c3nc4ccccc4n3C(C)C)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 2, 4, 5, 9, 9, 9, 9, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 9, 6, 6, 6, 14, 14, 14, 6, 6, 9, 9, 9, 9, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 9, 9, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 70 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545487620 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000545487620 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545487620/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545487620/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545487620 Building ZINC000545487620 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545487620' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545487620 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000545487620 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545487620/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545487620 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 488) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/488: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](c3nc4ccccc4n3C(C)C)C2)cc1Cl) `ZINC000545487620.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000545487620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545487620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000545487620 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](c3nc4ccccc4n3C(C)C)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 2, 5, 7, 10, 10, 10, 10, 10, 10, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 10, 6, 6, 6, 12, 12, 12, 6, 6, 10, 10, 10, 10, 10, 10, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 10, 10, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 73 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545487620 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545487620/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545487620 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 489) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/489: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](c3nc4ccccc4n3C(C)C)C2)cc1Cl) `ZINC000545487620.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000545487620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545487620/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000545487620 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](c3nc4ccccc4n3C(C)C)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 2, 4, 5, 9, 9, 9, 9, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 9, 6, 6, 6, 14, 14, 14, 6, 6, 9, 9, 9, 9, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 9, 9, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 70 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545487620 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000545487620 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545487620/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545487620/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545487620 Building ZINC000545494041 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545494041' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545494041 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000545494041 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545494041/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545494041 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 490) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/490 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/490' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2ncc(c3ccc(Cl)cc3)[nH]2)cc1Cl) `ZINC000545494041.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000545494041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545494041/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000545494041 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2ncc(c3ccc(Cl)cc3)[nH]2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 8, 6, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 4, 2, 4, 4, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 14, 14, 14, 14, 28, 28, 14, 14, 28, 28, 14, 14, 4, 4, 4, 11, 11, 11, 4, 4, 7, 7, 7, 7, 7, 7, 14, 28, 28, 28, 28, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545494041 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545494041/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545494041 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 491) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/491 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/491' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2ncc(c3ccc(Cl)cc3)[nH]2)cc1Cl) `ZINC000545494041.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000545494041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545494041/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000545494041 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2ncc(c3ccc(Cl)cc3)[nH]2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 8, 6, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 2, 5, 5, 1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 33, 33, 13, 13, 33, 33, 13, 13, 5, 5, 5, 12, 12, 12, 5, 5, 6, 6, 6, 6, 6, 6, 13, 33, 33, 33, 33, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545494041 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000545494041 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545494041/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545494041/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545494041 Building ZINC000545494041 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545494041' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545494041 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000545494041 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545494041/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545494041 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 490) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/490: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2ncc(c3ccc(Cl)cc3)[nH]2)cc1Cl) `ZINC000545494041.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000545494041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545494041/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000545494041 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2ncc(c3ccc(Cl)cc3)[nH]2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 8, 6, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 4, 2, 4, 4, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 14, 14, 14, 14, 28, 28, 14, 14, 28, 28, 14, 14, 4, 4, 4, 11, 11, 11, 4, 4, 7, 7, 7, 7, 7, 7, 14, 28, 28, 28, 28, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545494041 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545494041/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545494041 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 491) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/491: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2ncc(c3ccc(Cl)cc3)[nH]2)cc1Cl) `ZINC000545494041.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000545494041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545494041/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000545494041 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2ncc(c3ccc(Cl)cc3)[nH]2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 8, 6, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 2, 5, 5, 1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 33, 33, 13, 13, 33, 33, 13, 13, 5, 5, 5, 12, 12, 12, 5, 5, 6, 6, 6, 6, 6, 6, 13, 33, 33, 33, 33, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545494041 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000545494041 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545494041/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545494041/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545494041 Building ZINC000545494042 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545494042' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545494042 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000545494042 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545494042/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545494042 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 492) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/492 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/492' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2ncc(c3ccc(Cl)cc3)[nH]2)cc1Cl) `ZINC000545494042.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000545494042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545494042/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000545494042 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2ncc(c3ccc(Cl)cc3)[nH]2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 8, 6, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 13, 13, 13, 13, 32, 32, 14, 32, 32, 32, 13, 13, 6, 6, 6, 13, 13, 13, 6, 6, 5, 5, 5, 5, 5, 5, 13, 32, 32, 32, 32, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 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/129831/xbf-8058088.32/working/building/ZINC000545494042 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545494042/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545494042 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 493) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/493 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/493' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2ncc(c3ccc(Cl)cc3)[nH]2)cc1Cl) `ZINC000545494042.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000545494042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545494042/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000545494042 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2ncc(c3ccc(Cl)cc3)[nH]2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 8, 6, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 4, 2, 4, 4, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 13, 13, 13, 13, 28, 28, 13, 15, 28, 28, 13, 13, 4, 4, 4, 11, 11, 11, 4, 4, 7, 7, 7, 7, 7, 7, 13, 28, 28, 28, 28, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545494042 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000545494042 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545494042/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545494042/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545494042 Building ZINC000545494042 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545494042' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545494042 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000545494042 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545494042/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545494042 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 492) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/492: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2ncc(c3ccc(Cl)cc3)[nH]2)cc1Cl) `ZINC000545494042.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000545494042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545494042/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000545494042 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2ncc(c3ccc(Cl)cc3)[nH]2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 8, 6, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 13, 13, 13, 13, 32, 32, 14, 32, 32, 32, 13, 13, 6, 6, 6, 13, 13, 13, 6, 6, 5, 5, 5, 5, 5, 5, 13, 32, 32, 32, 32, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 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/129831/xbf-8058088.32/working/building/ZINC000545494042 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545494042/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545494042 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 493) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/493: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2ncc(c3ccc(Cl)cc3)[nH]2)cc1Cl) `ZINC000545494042.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000545494042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545494042/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000545494042 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2ncc(c3ccc(Cl)cc3)[nH]2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 8, 6, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 4, 2, 4, 4, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 13, 13, 13, 13, 28, 28, 13, 15, 28, 28, 13, 13, 4, 4, 4, 11, 11, 11, 4, 4, 7, 7, 7, 7, 7, 7, 13, 28, 28, 28, 28, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545494042 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000545494042 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545494042/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545494042/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545494042 Building ZINC000545506373 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545506373' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545506373 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000545506373 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545506373/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545506373 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 494) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/494 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/494' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(OCc3cccnc3)c(Cl)c2)cc1Cl) `ZINC000545506373.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000545506373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545506373/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000545506373 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(OCc3cccnc3)c(Cl)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 1, 16, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 8, 12, 29, 29, 29, 29, 29, 4, 4, 4, 2, 2, 2, 4, 4, 4, 2, 2, 1, 4, 4, 12, 12, 29, 29, 29, 29, 4, 2] 50 rigid atoms, others: [34, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545506373 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545506373/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545506373 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 495) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/495 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/495' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(OCc3cccnc3)c(Cl)c2)cc1Cl) `ZINC000545506373.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000545506373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545506373/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000545506373 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(OCc3cccnc3)c(Cl)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 1, 16, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 9, 12, 30, 29, 30, 30, 30, 4, 4, 4, 2, 2, 2, 4, 4, 4, 2, 2, 1, 4, 4, 12, 12, 30, 30, 30, 30, 4, 2] 50 rigid atoms, others: [34, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545506373 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000545506373 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545506373/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545506373/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545506373 Building ZINC000545506373 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545506373' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545506373 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000545506373 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545506373/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545506373 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 494) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/494: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(OCc3cccnc3)c(Cl)c2)cc1Cl) `ZINC000545506373.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000545506373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545506373/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000545506373 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(OCc3cccnc3)c(Cl)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 1, 16, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 8, 12, 29, 29, 29, 29, 29, 4, 4, 4, 2, 2, 2, 4, 4, 4, 2, 2, 1, 4, 4, 12, 12, 29, 29, 29, 29, 4, 2] 50 rigid atoms, others: [34, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545506373 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545506373/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545506373 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 495) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/495: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(OCc3cccnc3)c(Cl)c2)cc1Cl) `ZINC000545506373.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000545506373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545506373/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000545506373 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(OCc3cccnc3)c(Cl)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 1, 16, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 9, 12, 30, 29, 30, 30, 30, 4, 4, 4, 2, 2, 2, 4, 4, 4, 2, 2, 1, 4, 4, 12, 12, 30, 30, 30, 30, 4, 2] 50 rigid atoms, others: [34, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545506373 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000545506373 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545506373/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545506373/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545506373 Building ZINC000545509024 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545509024' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545509024 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000545509024 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545509024/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545509024 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 496) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/496 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/496' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(SCc3ccccc3Cl)cn2)cn1) `ZINC000545509024.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000545509024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545509024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000545509024 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(SCc3ccccc3Cl)cn2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', '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, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 5, 1, 1, 1, 1, 1, 1, 16, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 6, 6, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 15, 17, 25, 25, 25, 25, 25, 25, 4, 4, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 2, 4, 4, 17, 17, 25, 25, 25, 25, 4, 5] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545509024 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545509024/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545509024 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 497) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/497 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/497' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(SCc3ccccc3Cl)cn2)cn1) `ZINC000545509024.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000545509024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545509024/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000545509024 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(SCc3ccccc3Cl)cn2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', '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, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 5, 1, 1, 1, 1, 1, 1, 16, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 15, 18, 26, 26, 26, 26, 26, 26, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 4, 4, 18, 18, 26, 26, 26, 26, 4, 5] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545509024 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000545509024 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545509024/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545509024/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545509024 Building ZINC000545509024 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545509024' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545509024 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000545509024 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545509024/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545509024 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 496) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/496: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(SCc3ccccc3Cl)cn2)cn1) `ZINC000545509024.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000545509024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545509024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000545509024 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(SCc3ccccc3Cl)cn2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', '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, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 5, 1, 1, 1, 1, 1, 1, 16, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 6, 6, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 15, 17, 25, 25, 25, 25, 25, 25, 4, 4, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 2, 4, 4, 17, 17, 25, 25, 25, 25, 4, 5] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545509024 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545509024/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545509024 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 497) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/497: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(SCc3ccccc3Cl)cn2)cn1) `ZINC000545509024.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000545509024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545509024/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000545509024 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(SCc3ccccc3Cl)cn2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', '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, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 5, 1, 1, 1, 1, 1, 1, 16, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 15, 18, 26, 26, 26, 26, 26, 26, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 4, 4, 18, 18, 26, 26, 26, 26, 4, 5] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545509024 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000545509024 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545509024/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545509024/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000545509024 Building ZINC000469149610 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469149610' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469149610 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000469149610 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469149610/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469149610 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 498) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/498 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/498' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(=Cc2ccc(F)c(F)c2)CC1) `ZINC000469149610.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000469149610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469149610/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000469149610 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(=Cc2ccc(F)c(F)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 15, 1, 15, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 4, 5, 5, 2, 2, 1, 1, 1, 2, 4, 5, 10, 10, 10, 10, 10, 34, 34, 34, 34, 34, 34, 34, 10, 10, 2, 2, 2, 5, 5, 4, 5, 5, 2, 2, 2, 10, 10, 10, 10, 10, 34, 34, 34, 10, 10, 10, 10] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 66 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469149610 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469149610/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469149610 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 499) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/499 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/499' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(=Cc2ccc(F)c(F)c2)CC1) `ZINC000469149610.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000469149610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469149610/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000469149610 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(=Cc2ccc(F)c(F)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 15, 1, 15, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 2, 4, 5, 9, 9, 9, 9, 9, 33, 33, 33, 33, 33, 33, 33, 9, 9, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 9, 9, 9, 9, 9, 33, 33, 33, 9, 9, 9, 9] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469149610 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000469149610 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469149610/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469149610/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469149610 Building ZINC000469149610 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469149610' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469149610 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000469149610 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469149610/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469149610 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 498) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/498: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(=Cc2ccc(F)c(F)c2)CC1) `ZINC000469149610.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000469149610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469149610/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000469149610 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(=Cc2ccc(F)c(F)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 15, 1, 15, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 4, 5, 5, 2, 2, 1, 1, 1, 2, 4, 5, 10, 10, 10, 10, 10, 34, 34, 34, 34, 34, 34, 34, 10, 10, 2, 2, 2, 5, 5, 4, 5, 5, 2, 2, 2, 10, 10, 10, 10, 10, 34, 34, 34, 10, 10, 10, 10] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 66 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469149610 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469149610/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469149610 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 499) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/499: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(=Cc2ccc(F)c(F)c2)CC1) `ZINC000469149610.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000469149610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469149610/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000469149610 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(=Cc2ccc(F)c(F)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 15, 1, 15, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 2, 4, 5, 9, 9, 9, 9, 9, 33, 33, 33, 33, 33, 33, 33, 9, 9, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 9, 9, 9, 9, 9, 33, 33, 33, 9, 9, 9, 9] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469149610 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000469149610 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469149610/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469149610/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469149610 Building ZINC000469354279 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469354279' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469354279 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000469354279 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469354279/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469354279 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 500) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/500 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/500' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(c2ccccc2)sc1[C@H](C)N(C)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000469354279.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000469354279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469354279/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC000469354279 none Cc1nc(c2ccccc2)sc1[C@H](C)N(C)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 14, 1, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 26, 26, 22, 26, 26, 17, 12, 4, 12, 12, 3, 4, 1, 3, 1, 1, 1, 6, 6, 6, 6, 12, 12, 6, 12, 12, 6, 17, 17, 17, 26, 26, 22, 26, 26, 12, 12, 12, 4, 4, 4, 6, 12, 12, 12, 12, 12, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469354279 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469354279/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469354279 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 501) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/501 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/501' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(c2ccccc2)sc1[C@H](C)N(C)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000469354279.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000469354279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469354279/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC000469354279 none Cc1nc(c2ccccc2)sc1[C@H](C)N(C)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 14, 1, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 25, 25, 22, 25, 25, 22, 17, 5, 17, 17, 4, 5, 1, 4, 1, 1, 1, 6, 6, 6, 6, 12, 12, 6, 12, 12, 6, 22, 22, 22, 25, 25, 22, 25, 25, 17, 17, 17, 5, 5, 5, 6, 12, 12, 6, 12, 12, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469354279 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000469354279 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469354279/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469354279/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469354279 Building ZINC000469354279 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469354279' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469354279 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000469354279 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469354279/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469354279 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 500) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/500: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(c2ccccc2)sc1[C@H](C)N(C)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000469354279.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000469354279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469354279/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC000469354279 none Cc1nc(c2ccccc2)sc1[C@H](C)N(C)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 14, 1, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 26, 26, 22, 26, 26, 17, 12, 4, 12, 12, 3, 4, 1, 3, 1, 1, 1, 6, 6, 6, 6, 12, 12, 6, 12, 12, 6, 17, 17, 17, 26, 26, 22, 26, 26, 12, 12, 12, 4, 4, 4, 6, 12, 12, 12, 12, 12, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469354279 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469354279/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469354279 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 501) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/501: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(c2ccccc2)sc1[C@H](C)N(C)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000469354279.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000469354279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469354279/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC000469354279 none Cc1nc(c2ccccc2)sc1[C@H](C)N(C)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 14, 1, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 25, 25, 22, 25, 25, 22, 17, 5, 17, 17, 4, 5, 1, 4, 1, 1, 1, 6, 6, 6, 6, 12, 12, 6, 12, 12, 6, 22, 22, 22, 25, 25, 22, 25, 25, 17, 17, 17, 5, 5, 5, 6, 12, 12, 6, 12, 12, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469354279 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000469354279 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469354279/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469354279/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469354279 Building ZINC000469354281 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469354281' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469354281 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000469354281 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469354281/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469354281 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 502) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/502 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/502' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(c2ccccc2)sc1[C@@H](C)N(C)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000469354281.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000469354281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469354281/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC000469354281 none Cc1nc(c2ccccc2)sc1[C@@H](C)N(C)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 14, 1, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 25, 25, 23, 25, 25, 22, 17, 5, 17, 17, 4, 5, 1, 4, 1, 1, 1, 6, 6, 6, 6, 12, 12, 6, 12, 12, 6, 22, 22, 22, 25, 25, 25, 25, 25, 17, 17, 17, 5, 5, 5, 6, 12, 12, 6, 12, 12, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469354281 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469354281/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469354281 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 503) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/503 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/503' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(c2ccccc2)sc1[C@@H](C)N(C)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000469354281.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000469354281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469354281/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC000469354281 none Cc1nc(c2ccccc2)sc1[C@@H](C)N(C)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 14, 1, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 26, 26, 22, 26, 26, 17, 12, 4, 12, 12, 3, 4, 1, 3, 1, 1, 1, 6, 6, 6, 6, 12, 12, 6, 12, 12, 6, 17, 17, 17, 26, 26, 22, 26, 26, 12, 12, 12, 4, 4, 4, 6, 12, 12, 6, 12, 12, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469354281 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000469354281 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469354281/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469354281/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469354281 Building ZINC000469354281 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469354281' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469354281 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000469354281 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469354281/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469354281 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 502) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/502: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(c2ccccc2)sc1[C@@H](C)N(C)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000469354281.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000469354281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469354281/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC000469354281 none Cc1nc(c2ccccc2)sc1[C@@H](C)N(C)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 14, 1, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 25, 25, 23, 25, 25, 22, 17, 5, 17, 17, 4, 5, 1, 4, 1, 1, 1, 6, 6, 6, 6, 12, 12, 6, 12, 12, 6, 22, 22, 22, 25, 25, 25, 25, 25, 17, 17, 17, 5, 5, 5, 6, 12, 12, 6, 12, 12, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469354281 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469354281/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469354281 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 503) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/503: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(c2ccccc2)sc1[C@@H](C)N(C)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000469354281.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000469354281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469354281/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC000469354281 none Cc1nc(c2ccccc2)sc1[C@@H](C)N(C)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 14, 1, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 26, 26, 22, 26, 26, 17, 12, 4, 12, 12, 3, 4, 1, 3, 1, 1, 1, 6, 6, 6, 6, 12, 12, 6, 12, 12, 6, 17, 17, 17, 26, 26, 22, 26, 26, 12, 12, 12, 4, 4, 4, 6, 12, 12, 6, 12, 12, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469354281 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000469354281 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469354281/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469354281/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469354281 Building ZINC000546153469 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153469' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153469 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546153469 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153469/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153469 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 504) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/504 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/504' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2csc(NC(=O)[C@@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)n2)cc1Cl) `ZINC000546153469.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546153469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000546153469 none COc1ccc(c2csc(NC(=O)[C@@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)n2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 8, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 18, 12, 18, 18, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 7, 4, 4, 4, 4, 18, 18, 18, 29, 29, 29, 18, 18, 4, 2, 4, 4, 7, 7, 7, 4, 18] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153469 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153469/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153469 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 505) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/505 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/505' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2csc(NC(=O)[C@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)n2)cc1Cl) `ZINC000546153469.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546153469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153469/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000546153469 none COc1ccc(c2csc(NC(=O)[C@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)n2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 8, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 18, 12, 18, 18, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 7, 4, 4, 4, 4, 18, 18, 18, 29, 29, 29, 18, 18, 4, 2, 4, 4, 7, 7, 7, 4, 18] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153469 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546153469 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153469/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153469/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153469 Building ZINC000546153469 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153469' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153469 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546153469 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153469/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153469 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 504) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/504: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2csc(NC(=O)[C@@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)n2)cc1Cl) `ZINC000546153469.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546153469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000546153469 none COc1ccc(c2csc(NC(=O)[C@@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)n2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 8, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 18, 12, 18, 18, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 7, 4, 4, 4, 4, 18, 18, 18, 29, 29, 29, 18, 18, 4, 2, 4, 4, 7, 7, 7, 4, 18] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153469 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153469/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153469 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 505) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/505: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2csc(NC(=O)[C@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)n2)cc1Cl) `ZINC000546153469.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546153469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153469/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000546153469 none COc1ccc(c2csc(NC(=O)[C@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)n2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 8, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 18, 12, 18, 18, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 7, 4, 4, 4, 4, 18, 18, 18, 29, 29, 29, 18, 18, 4, 2, 4, 4, 7, 7, 7, 4, 18] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153469 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546153469 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153469/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153469/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153469 Building ZINC000546153494 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153494' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153494 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546153494 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153494/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153494 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 506) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/506 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/506' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2nc(c3ccc(OC(F)F)cc3)cs2)cc1Cl) `ZINC000546153494.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546153494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000546153494 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2nc(c3ccc(OC(F)F)cc3)cs2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 1, 14, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 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: [5, 3, 2, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 11, 11, 4, 4, 24, 29, 29, 11, 11, 4, 4, 3, 3, 3, 5, 5, 5, 3, 3, 2, 11, 11, 29, 11, 11, 4, 3] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153494 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153494/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153494 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 507) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/507 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/507' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2nc(c3ccc(OC(F)F)cc3)cs2)cc1Cl) `ZINC000546153494.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546153494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153494/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000546153494 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2nc(c3ccc(OC(F)F)cc3)cs2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 1, 14, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 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: [6, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 10, 10, 4, 4, 23, 28, 28, 10, 10, 4, 4, 4, 4, 4, 6, 6, 6, 4, 4, 2, 10, 10, 28, 10, 10, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153494 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546153494 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153494/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153494/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153494 Building ZINC000546153494 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153494' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153494 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546153494 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153494/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153494 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 506) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/506: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2nc(c3ccc(OC(F)F)cc3)cs2)cc1Cl) `ZINC000546153494.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546153494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000546153494 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2nc(c3ccc(OC(F)F)cc3)cs2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 1, 14, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 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: [5, 3, 2, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 11, 11, 4, 4, 24, 29, 29, 11, 11, 4, 4, 3, 3, 3, 5, 5, 5, 3, 3, 2, 11, 11, 29, 11, 11, 4, 3] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153494 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153494/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153494 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 507) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/507: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2nc(c3ccc(OC(F)F)cc3)cs2)cc1Cl) `ZINC000546153494.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546153494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153494/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000546153494 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2nc(c3ccc(OC(F)F)cc3)cs2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 1, 14, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 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: [6, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 10, 10, 4, 4, 23, 28, 28, 10, 10, 4, 4, 4, 4, 4, 6, 6, 6, 4, 4, 2, 10, 10, 28, 10, 10, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153494 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546153494 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153494/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153494/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153494 Building ZINC000546153206 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153206' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153206 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546153206 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153206/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153206 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 508) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/508 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/508' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(Cc1ccccc1)[C@H](C)c1cccc(NC(C)=O)c1) `ZINC000546153206.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546153206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000546153206 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(Cc1ccccc1)[C@H](C)c1cccc(NC(C)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 8, 1, 5, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 3, 3, 6, 7, 7, 7, 7, 7, 7, 6, 9, 9, 9, 24, 24, 24, 24, 24, 33, 33, 33, 24, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 9, 9, 9, 24, 24, 24, 33, 33, 33, 33, 24] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153206 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153206/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153206 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 509) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/509 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/509' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(Cc1ccccc1)[C@H](C)c1cccc(NC(C)=O)c1) `ZINC000546153206.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546153206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153206/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000546153206 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(Cc1ccccc1)[C@H](C)c1cccc(NC(C)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 8, 1, 5, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 5, 5, 7, 10, 10, 10, 10, 10, 10, 7, 12, 12, 12, 30, 30, 30, 30, 30, 37, 37, 37, 30, 3, 3, 3, 3, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 12, 12, 12, 30, 30, 30, 37, 37, 37, 37, 30] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 128 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153206 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546153206 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153206/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153206/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153206 Building ZINC000546153206 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153206' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153206 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546153206 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153206/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153206 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 508) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/508: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(Cc1ccccc1)[C@H](C)c1cccc(NC(C)=O)c1) `ZINC000546153206.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546153206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000546153206 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(Cc1ccccc1)[C@H](C)c1cccc(NC(C)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 8, 1, 5, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 3, 3, 6, 7, 7, 7, 7, 7, 7, 6, 9, 9, 9, 24, 24, 24, 24, 24, 33, 33, 33, 24, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 9, 9, 9, 24, 24, 24, 33, 33, 33, 33, 24] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153206 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153206/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153206 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 509) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/509: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(Cc1ccccc1)[C@H](C)c1cccc(NC(C)=O)c1) `ZINC000546153206.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546153206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153206/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000546153206 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(Cc1ccccc1)[C@H](C)c1cccc(NC(C)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 8, 1, 5, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 5, 5, 7, 10, 10, 10, 10, 10, 10, 7, 12, 12, 12, 30, 30, 30, 30, 30, 37, 37, 37, 30, 3, 3, 3, 3, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 12, 12, 12, 30, 30, 30, 37, 37, 37, 37, 30] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 128 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153206 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546153206 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153206/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153206/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153206 Building ZINC000546153207 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153207' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153207 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546153207 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153207/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153207 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 510) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/510 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/510' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(Cc1ccccc1)[C@@H](C)c1cccc(NC(C)=O)c1) `ZINC000546153207.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546153207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153207/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000546153207 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(Cc1ccccc1)[C@@H](C)c1cccc(NC(C)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 8, 1, 5, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 5, 5, 10, 13, 13, 13, 13, 13, 13, 10, 15, 15, 15, 31, 31, 31, 31, 31, 37, 37, 37, 31, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 15, 15, 15, 31, 31, 31, 37, 37, 37, 37, 31] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 131 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153207 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153207/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153207 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 511) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/511 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/511' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(Cc1ccccc1)[C@@H](C)c1cccc(NC(C)=O)c1) `ZINC000546153207.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546153207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153207/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000546153207 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(Cc1ccccc1)[C@@H](C)c1cccc(NC(C)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 8, 1, 5, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 3, 3, 6, 7, 7, 7, 7, 7, 7, 6, 9, 9, 9, 24, 24, 24, 24, 24, 33, 33, 33, 24, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 9, 9, 9, 24, 24, 24, 33, 33, 33, 33, 24] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153207 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546153207 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153207/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153207/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153207 Building ZINC000546153207 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153207' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153207 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546153207 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153207/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153207 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 510) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/510: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(Cc1ccccc1)[C@@H](C)c1cccc(NC(C)=O)c1) `ZINC000546153207.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546153207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153207/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000546153207 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(Cc1ccccc1)[C@@H](C)c1cccc(NC(C)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 8, 1, 5, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 5, 5, 10, 13, 13, 13, 13, 13, 13, 10, 15, 15, 15, 31, 31, 31, 31, 31, 37, 37, 37, 31, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 15, 15, 15, 31, 31, 31, 37, 37, 37, 37, 31] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 131 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153207 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153207/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153207 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 511) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/511: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(Cc1ccccc1)[C@@H](C)c1cccc(NC(C)=O)c1) `ZINC000546153207.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546153207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153207/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000546153207 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(Cc1ccccc1)[C@@H](C)c1cccc(NC(C)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 8, 1, 5, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 3, 3, 6, 7, 7, 7, 7, 7, 7, 6, 9, 9, 9, 24, 24, 24, 24, 24, 33, 33, 33, 24, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 9, 9, 9, 24, 24, 24, 33, 33, 33, 33, 24] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153207 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546153207 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153207/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153207/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546153207 Building ZINC000546154161 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546154161' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546154161 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546154161 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546154161/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546154161 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 512) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/512 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/512' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2cccs2)Cc2ccccc2OC)cc1Cl) `ZINC000546154161.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546154161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546154161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000546154161 none COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2cccs2)Cc2ccccc2OC)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 14, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 3, 6, 9, 9, 9, 9, 3, 7, 10, 10, 8, 10, 10, 10, 16, 4, 4, 4, 7, 7, 7, 4, 4, 6, 6, 9, 9, 9, 7, 7, 10, 10, 10, 10, 16, 16, 16, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546154161 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546154161/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546154161 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 513) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/513 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/513' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2cccs2)Cc2ccccc2OC)cc1Cl) `ZINC000546154161.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546154161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546154161/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000546154161 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2cccs2)Cc2ccccc2OC)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 14, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 3, 6, 9, 9, 9, 9, 3, 7, 10, 10, 10, 10, 10, 10, 16, 4, 4, 4, 7, 7, 7, 4, 4, 6, 6, 9, 9, 9, 7, 7, 10, 10, 10, 10, 16, 16, 16, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546154161 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546154161 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546154161/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546154161/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546154161 Building ZINC000546154161 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546154161' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546154161 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546154161 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546154161/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546154161 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 512) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/512: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2cccs2)Cc2ccccc2OC)cc1Cl) `ZINC000546154161.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546154161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546154161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000546154161 none COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2cccs2)Cc2ccccc2OC)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 14, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 3, 6, 9, 9, 9, 9, 3, 7, 10, 10, 8, 10, 10, 10, 16, 4, 4, 4, 7, 7, 7, 4, 4, 6, 6, 9, 9, 9, 7, 7, 10, 10, 10, 10, 16, 16, 16, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546154161 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546154161/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546154161 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 513) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/513: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2cccs2)Cc2ccccc2OC)cc1Cl) `ZINC000546154161.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546154161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546154161/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000546154161 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2cccs2)Cc2ccccc2OC)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 14, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 3, 6, 9, 9, 9, 9, 3, 7, 10, 10, 10, 10, 10, 10, 16, 4, 4, 4, 7, 7, 7, 4, 4, 6, 6, 9, 9, 9, 7, 7, 10, 10, 10, 10, 16, 16, 16, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546154161 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546154161 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546154161/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546154161/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546154161 Building ZINC000546164435 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546164435' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546164435 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546164435 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546164435/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546164435 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 514) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/514 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/514' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2csc(Br)c2)C2CC2)cc1Cl) `ZINC000546164435.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546164435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546164435/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000546164435 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2csc(Br)c2)C2CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'Br', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 14, 1, 17, 1, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 4, 5, 14, 14, 14, 14, 14, 4, 4, 4, 5, 5, 5, 9, 9, 9, 5, 5, 5, 5, 14, 14, 4, 4, 4, 4, 4, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546164435 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546164435/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546164435 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 515) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/515 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/515' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2csc(Br)c2)C2CC2)cc1Cl) `ZINC000546164435.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546164435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546164435/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000546164435 none COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2csc(Br)c2)C2CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'Br', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 14, 1, 17, 1, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 2, 2, 3, 5, 13, 13, 13, 13, 13, 3, 5, 5, 6, 6, 6, 12, 12, 12, 6, 6, 5, 5, 13, 13, 5, 5, 5, 5, 5, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546164435 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546164435 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546164435/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546164435/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546164435 Building ZINC000546164435 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546164435' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546164435 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546164435 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546164435/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546164435 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 514) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/514: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2csc(Br)c2)C2CC2)cc1Cl) `ZINC000546164435.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546164435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546164435/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000546164435 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2csc(Br)c2)C2CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'Br', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 14, 1, 17, 1, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 4, 5, 14, 14, 14, 14, 14, 4, 4, 4, 5, 5, 5, 9, 9, 9, 5, 5, 5, 5, 14, 14, 4, 4, 4, 4, 4, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546164435 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546164435/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546164435 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 515) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/515: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2csc(Br)c2)C2CC2)cc1Cl) `ZINC000546164435.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546164435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546164435/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000546164435 none COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2csc(Br)c2)C2CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'Br', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 14, 1, 17, 1, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 2, 2, 3, 5, 13, 13, 13, 13, 13, 3, 5, 5, 6, 6, 6, 12, 12, 12, 6, 6, 5, 5, 13, 13, 5, 5, 5, 5, 5, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546164435 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546164435 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546164435/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546164435/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546164435 Building ZINC000546167088 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546167088' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546167088 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546167088 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546167088/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546167088 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 516) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/516 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/516' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(Cc1cccc(C(F)(F)F)c1)Cc1ccccn1) `ZINC000546167088.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546167088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546167088/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000546167088 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(Cc1cccc(C(F)(F)F)c1)Cc1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 2, 2, 4, 10, 26, 26, 18, 26, 26, 26, 26, 26, 25, 4, 8, 11, 11, 11, 11, 11, 3, 3, 3, 3, 3, 3, 3, 10, 10, 26, 26, 18, 26, 8, 8, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546167088 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546167088/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546167088 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 517) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/517 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/517' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(Cc1cccc(C(F)(F)F)c1)Cc1ccccn1) `ZINC000546167088.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546167088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546167088/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000546167088 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(Cc1cccc(C(F)(F)F)c1)Cc1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 2, 2, 4, 10, 26, 26, 26, 26, 26, 26, 26, 26, 25, 4, 8, 11, 11, 11, 11, 11, 3, 3, 3, 3, 3, 3, 3, 10, 10, 26, 26, 26, 26, 8, 8, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546167088 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546167088 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546167088/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546167088/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546167088 Building ZINC000546167088 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546167088' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546167088 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546167088 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546167088/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546167088 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 516) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/516: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(Cc1cccc(C(F)(F)F)c1)Cc1ccccn1) `ZINC000546167088.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546167088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546167088/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000546167088 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(Cc1cccc(C(F)(F)F)c1)Cc1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 2, 2, 4, 10, 26, 26, 18, 26, 26, 26, 26, 26, 25, 4, 8, 11, 11, 11, 11, 11, 3, 3, 3, 3, 3, 3, 3, 10, 10, 26, 26, 18, 26, 8, 8, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546167088 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546167088/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546167088 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 517) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/517: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(Cc1cccc(C(F)(F)F)c1)Cc1ccccn1) `ZINC000546167088.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546167088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546167088/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000546167088 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(Cc1cccc(C(F)(F)F)c1)Cc1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 2, 2, 4, 10, 26, 26, 26, 26, 26, 26, 26, 26, 25, 4, 8, 11, 11, 11, 11, 11, 3, 3, 3, 3, 3, 3, 3, 10, 10, 26, 26, 26, 26, 8, 8, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546167088 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546167088 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546167088/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546167088/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546167088 Building ZINC000546166785 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546166785' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546166785 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546166785 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546166785/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546166785 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 518) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/518 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/518' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccccc2OC)cc1OCc1ccc2ccccc2n1) `ZINC000546166785.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546166785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546166785/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000546166785 none COc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccccc2OC)cc1OCc1ccc2ccccc2n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 7, 7, 7, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 7, 7, 7, 33, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 7, 44, 44, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546166785 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546166785/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546166785 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 519) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/519 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/519' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)cc1OCc1ccc2ccccc2n1) `ZINC000546166785.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546166785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546166785/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000546166785 none COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)cc1OCc1ccc2ccccc2n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 7, 7, 7, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 7, 7, 7, 31, 43, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 7, 43, 43, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546166785 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546166785 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546166785/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546166785/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546166785 Building ZINC000546166785 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546166785' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546166785 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546166785 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546166785/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546166785 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 518) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/518: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccccc2OC)cc1OCc1ccc2ccccc2n1) `ZINC000546166785.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546166785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546166785/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000546166785 none COc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccccc2OC)cc1OCc1ccc2ccccc2n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 7, 7, 7, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 7, 7, 7, 33, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 7, 44, 44, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546166785 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546166785/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546166785 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 519) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/519: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)cc1OCc1ccc2ccccc2n1) `ZINC000546166785.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546166785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546166785/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000546166785 none COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)cc1OCc1ccc2ccccc2n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 7, 7, 7, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 7, 7, 7, 31, 43, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 7, 43, 43, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546166785 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546166785 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546166785/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546166785/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546166785 Building ZINC000546183976 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183976' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183976 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546183976 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183976/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183976 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 520) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/520 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/520' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](c2ccccc2OC(F)F)C(F)(F)F)cc1Cl) `ZINC000546183976.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546183976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183976/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000546183976 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](c2ccccc2OC(F)F)C(F)(F)F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 5, 15, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 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: [16, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 8, 8, 5, 8, 8, 8, 18, 25, 25, 5, 5, 5, 5, 6, 6, 6, 16, 16, 16, 6, 6, 3, 8, 8, 8, 8, 25, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 127 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183976 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183976/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183976 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 521) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/521 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/521' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](c2ccccc2OC(F)F)C(F)(F)F)cc1Cl) `ZINC000546183976.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546183976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183976/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000546183976 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](c2ccccc2OC(F)F)C(F)(F)F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 5, 15, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 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: [13, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 6, 6, 11, 11, 7, 11, 11, 11, 22, 23, 23, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 6, 6, 3, 11, 11, 11, 11, 23, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 109 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183976 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546183976 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183976/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183976/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183976 Building ZINC000546183976 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183976' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183976 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546183976 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183976/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183976 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 520) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/520: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](c2ccccc2OC(F)F)C(F)(F)F)cc1Cl) `ZINC000546183976.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546183976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183976/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000546183976 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](c2ccccc2OC(F)F)C(F)(F)F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 5, 15, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 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: [16, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 8, 8, 5, 8, 8, 8, 18, 25, 25, 5, 5, 5, 5, 6, 6, 6, 16, 16, 16, 6, 6, 3, 8, 8, 8, 8, 25, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 127 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183976 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183976/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183976 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 521) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/521: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](c2ccccc2OC(F)F)C(F)(F)F)cc1Cl) `ZINC000546183976.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546183976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183976/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000546183976 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](c2ccccc2OC(F)F)C(F)(F)F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 5, 15, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 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: [13, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 6, 6, 11, 11, 7, 11, 11, 11, 22, 23, 23, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 6, 6, 3, 11, 11, 11, 11, 23, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 109 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183976 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546183976 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183976/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183976/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183976 Building ZINC000546183981 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183981' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183981 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546183981 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183981/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183981 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 522) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/522 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/522' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](c2ccccc2OC(F)F)C(F)(F)F)cc1Cl) `ZINC000546183981.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546183981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183981/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000546183981 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](c2ccccc2OC(F)F)C(F)(F)F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 5, 15, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 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: [13, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 6, 6, 11, 11, 7, 11, 11, 11, 22, 24, 24, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 6, 6, 3, 11, 11, 11, 11, 24, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 115 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183981 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183981/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183981 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 523) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/523 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/523' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](c2ccccc2OC(F)F)C(F)(F)F)cc1Cl) `ZINC000546183981.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546183981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183981/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000546183981 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](c2ccccc2OC(F)F)C(F)(F)F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 5, 15, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 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: [16, 6, 3, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 8, 8, 5, 8, 8, 8, 18, 25, 25, 5, 5, 5, 5, 6, 6, 6, 16, 16, 16, 6, 6, 3, 8, 8, 8, 8, 25, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 125 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183981 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546183981 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183981/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183981/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183981 Building ZINC000546183981 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183981' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183981 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546183981 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183981/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183981 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 522) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/522: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](c2ccccc2OC(F)F)C(F)(F)F)cc1Cl) `ZINC000546183981.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546183981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183981/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000546183981 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](c2ccccc2OC(F)F)C(F)(F)F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 5, 15, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 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: [13, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 6, 6, 11, 11, 7, 11, 11, 11, 22, 24, 24, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 6, 6, 3, 11, 11, 11, 11, 24, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 115 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183981 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183981/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183981 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 523) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/523: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](c2ccccc2OC(F)F)C(F)(F)F)cc1Cl) `ZINC000546183981.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546183981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183981/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000546183981 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](c2ccccc2OC(F)F)C(F)(F)F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 5, 15, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 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: [16, 6, 3, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 8, 8, 5, 8, 8, 8, 18, 25, 25, 5, 5, 5, 5, 6, 6, 6, 16, 16, 16, 6, 6, 3, 8, 8, 8, 8, 25, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 125 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183981 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546183981 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183981/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183981/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183981 Building ZINC000546184037 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184037' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184037 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546184037 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184037/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184037 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 524) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/524 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/524' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2ccccc2OC)[C@@H]2CCCC[C@@H]2C)cc1OC) `ZINC000546184037.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546184037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184037/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000546184037 none COc1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2ccccc2OC)[C@@H]2CCCC[C@@H]2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 5, 5, 7, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 14, 6, 4, 2, 1, 2, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 14, 14, 14, 35, 31, 31, 31, 14, 14, 6, 6, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 14, 35, 35, 35] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 117 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184037 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184037/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184037 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 525) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/525 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/525' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN(C(=O)[C@]([O-])([SiH3])c2ccccc2OC)[C@@H]2CCCC[C@@H]2C)cc1OC) `ZINC000546184037.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546184037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184037/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000546184037 none COc1ccc(CN(C(=O)[C@]([O-])([SiH3])c2ccccc2OC)[C@@H]2CCCC[C@@H]2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 5, 5, 7, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [22, 10, 10, 10, 10, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 10, 22, 22, 22, 22, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 22, 22, 22] 40 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 83 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184037 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546184037 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184037/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184037/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184037 Building ZINC000546184037 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184037' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184037 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546184037 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184037/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184037 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 524) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/524: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2ccccc2OC)[C@@H]2CCCC[C@@H]2C)cc1OC) `ZINC000546184037.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546184037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184037/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000546184037 none COc1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2ccccc2OC)[C@@H]2CCCC[C@@H]2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 5, 5, 7, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 14, 6, 4, 2, 1, 2, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 14, 14, 14, 35, 31, 31, 31, 14, 14, 6, 6, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 14, 35, 35, 35] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 117 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184037 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184037/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184037 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 525) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/525: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN(C(=O)[C@]([O-])([SiH3])c2ccccc2OC)[C@@H]2CCCC[C@@H]2C)cc1OC) `ZINC000546184037.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546184037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184037/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000546184037 none COc1ccc(CN(C(=O)[C@]([O-])([SiH3])c2ccccc2OC)[C@@H]2CCCC[C@@H]2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 5, 5, 7, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [22, 10, 10, 10, 10, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 10, 22, 22, 22, 22, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 22, 22, 22] 40 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 83 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184037 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546184037 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184037/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184037/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184037 Building ZINC000546184038 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184038' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184038 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546184038 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184038/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184038 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 526) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/526 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/526' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2ccccc2OC)[C@H]2CCCC[C@@H]2C)cc1OC) `ZINC000546184038.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546184038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000546184038 none COc1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2ccccc2OC)[C@H]2CCCC[C@@H]2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 5, 5, 7, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 26, 26, 26, 26, 13, 7, 4, 1, 4, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 26, 26, 26, 43, 43, 43, 43, 26, 26, 13, 13, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 26, 43, 43, 43] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 151 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184038 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184038/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184038 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 527) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/527 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/527' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN(C(=O)[C@]([O-])([SiH3])c2ccccc2OC)[C@H]2CCCC[C@@H]2C)cc1OC) `ZINC000546184038.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546184038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184038/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000546184038 none COc1ccc(CN(C(=O)[C@]([O-])([SiH3])c2ccccc2OC)[C@H]2CCCC[C@@H]2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 5, 5, 7, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 17, 17, 17, 17, 8, 6, 4, 1, 4, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 17, 17, 17, 31, 31, 31, 31, 17, 17, 8, 8, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 17, 31, 31, 31] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184038 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546184038 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184038/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184038/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184038 Building ZINC000546184038 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184038' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184038 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546184038 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184038/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184038 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 526) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/526: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2ccccc2OC)[C@H]2CCCC[C@@H]2C)cc1OC) `ZINC000546184038.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546184038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000546184038 none COc1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2ccccc2OC)[C@H]2CCCC[C@@H]2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 5, 5, 7, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 26, 26, 26, 26, 13, 7, 4, 1, 4, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 26, 26, 26, 43, 43, 43, 43, 26, 26, 13, 13, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 26, 43, 43, 43] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 151 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184038 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184038/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184038 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 527) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/527: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN(C(=O)[C@]([O-])([SiH3])c2ccccc2OC)[C@H]2CCCC[C@@H]2C)cc1OC) `ZINC000546184038.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546184038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184038/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000546184038 none COc1ccc(CN(C(=O)[C@]([O-])([SiH3])c2ccccc2OC)[C@H]2CCCC[C@@H]2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 5, 5, 7, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 17, 17, 17, 17, 8, 6, 4, 1, 4, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 17, 17, 17, 31, 31, 31, 31, 17, 17, 8, 8, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 17, 31, 31, 31] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184038 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546184038 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184038/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184038/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184038 Building ZINC000546184039 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184039' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184039 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546184039 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184039/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184039 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 528) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/528 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/528' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2ccccc2OC)[C@H]2CCCC[C@H]2C)cc1OC) `ZINC000546184039.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546184039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000546184039 none COc1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2ccccc2OC)[C@H]2CCCC[C@H]2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 5, 5, 7, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [26, 12, 12, 12, 12, 5, 5, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 4, 4, 4, 5, 7, 7, 7, 7, 7, 7, 7, 7, 12, 12, 12, 26, 26, 26, 26, 12, 12, 5, 5, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 12, 26, 26, 26] 44 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 97 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184039 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184039/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184039 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 529) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/529 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/529' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN(C(=O)[C@]([O-])([SiH3])c2ccccc2OC)[C@H]2CCCC[C@H]2C)cc1OC) `ZINC000546184039.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546184039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184039/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000546184039 none COc1ccc(CN(C(=O)[C@]([O-])([SiH3])c2ccccc2OC)[C@H]2CCCC[C@H]2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 5, 5, 7, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 15, 15, 15, 5, 4, 2, 1, 2, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 15, 15, 15, 37, 34, 34, 34, 15, 15, 5, 5, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 15, 37, 37, 37] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 120 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184039 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546184039 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184039/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184039/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184039 Building ZINC000546184039 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184039' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184039 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546184039 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184039/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184039 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 528) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/528: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2ccccc2OC)[C@H]2CCCC[C@H]2C)cc1OC) `ZINC000546184039.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546184039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000546184039 none COc1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2ccccc2OC)[C@H]2CCCC[C@H]2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 5, 5, 7, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [26, 12, 12, 12, 12, 5, 5, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 4, 4, 4, 5, 7, 7, 7, 7, 7, 7, 7, 7, 12, 12, 12, 26, 26, 26, 26, 12, 12, 5, 5, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 12, 26, 26, 26] 44 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 97 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184039 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184039/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184039 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 529) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/529: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN(C(=O)[C@]([O-])([SiH3])c2ccccc2OC)[C@H]2CCCC[C@H]2C)cc1OC) `ZINC000546184039.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546184039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184039/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000546184039 none COc1ccc(CN(C(=O)[C@]([O-])([SiH3])c2ccccc2OC)[C@H]2CCCC[C@H]2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 5, 5, 7, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 15, 15, 15, 5, 4, 2, 1, 2, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 15, 15, 15, 37, 34, 34, 34, 15, 15, 5, 5, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 15, 37, 37, 37] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 120 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184039 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546184039 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184039/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184039/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184039 Building ZINC000546184040 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184040' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184040 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546184040 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184040/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184040 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 530) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/530 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/530' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2ccccc2OC)[C@@H]2CCCC[C@H]2C)cc1OC) `ZINC000546184040.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546184040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184040/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000546184040 none COc1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2ccccc2OC)[C@@H]2CCCC[C@H]2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 5, 5, 7, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 16, 16, 7, 5, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 16, 16, 16, 32, 32, 32, 32, 16, 16, 7, 7, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 16, 32, 32, 32] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184040 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184040/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184040 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 531) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/531 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/531' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN(C(=O)[C@]([O-])([SiH3])c2ccccc2OC)[C@@H]2CCCC[C@H]2C)cc1OC) `ZINC000546184040.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546184040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184040/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000546184040 none COc1ccc(CN(C(=O)[C@]([O-])([SiH3])c2ccccc2OC)[C@@H]2CCCC[C@H]2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 5, 5, 7, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [41, 24, 24, 24, 24, 11, 6, 4, 1, 4, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 41, 41, 41, 41, 24, 24, 11, 11, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 41, 41, 41] 46 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 140 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184040 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546184040 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184040/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184040/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184040 Building ZINC000546184040 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184040' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184040 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546184040 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184040/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184040 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 530) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/530: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2ccccc2OC)[C@@H]2CCCC[C@H]2C)cc1OC) `ZINC000546184040.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546184040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184040/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000546184040 none COc1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2ccccc2OC)[C@@H]2CCCC[C@H]2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 5, 5, 7, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 16, 16, 7, 5, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 16, 16, 16, 32, 32, 32, 32, 16, 16, 7, 7, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 16, 32, 32, 32] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184040 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184040/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184040 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 531) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/531: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN(C(=O)[C@]([O-])([SiH3])c2ccccc2OC)[C@@H]2CCCC[C@H]2C)cc1OC) `ZINC000546184040.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546184040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184040/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000546184040 none COc1ccc(CN(C(=O)[C@]([O-])([SiH3])c2ccccc2OC)[C@@H]2CCCC[C@H]2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 5, 5, 7, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [41, 24, 24, 24, 24, 11, 6, 4, 1, 4, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 41, 41, 41, 41, 24, 24, 11, 11, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 41, 41, 41] 46 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 140 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184040 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546184040 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184040/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184040/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546184040 Building ZINC000546183848 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183848' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183848 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546183848 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183848/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183848 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 532) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/532 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/532' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cccc(C(=O)Nc3cccc(F)c3)c2)cc1Cl) `ZINC000546183848.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546183848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000546183848 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cccc(C(=O)Nc3cccc(F)c3)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 6, 6, 6, 24, 24, 24, 24, 24, 24, 4, 4, 4, 4, 7, 7, 7, 4, 4, 2, 4, 4, 4, 6, 24, 24, 24, 24, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183848 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183848/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183848 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 533) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/533 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/533' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cccc(C(=O)Nc3cccc(F)c3)c2)cc1Cl) `ZINC000546183848.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546183848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183848/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000546183848 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cccc(C(=O)Nc3cccc(F)c3)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 6, 6, 6, 23, 23, 23, 23, 23, 23, 4, 4, 4, 4, 7, 7, 7, 4, 4, 2, 4, 4, 4, 6, 23, 23, 23, 23, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183848 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546183848 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183848/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183848/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183848 Building ZINC000546183848 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183848' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183848 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546183848 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183848/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183848 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 532) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/532: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cccc(C(=O)Nc3cccc(F)c3)c2)cc1Cl) `ZINC000546183848.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546183848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000546183848 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cccc(C(=O)Nc3cccc(F)c3)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 6, 6, 6, 24, 24, 24, 24, 24, 24, 4, 4, 4, 4, 7, 7, 7, 4, 4, 2, 4, 4, 4, 6, 24, 24, 24, 24, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183848 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183848/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183848 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 533) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/533: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cccc(C(=O)Nc3cccc(F)c3)c2)cc1Cl) `ZINC000546183848.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546183848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183848/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000546183848 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cccc(C(=O)Nc3cccc(F)c3)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 6, 6, 6, 23, 23, 23, 23, 23, 23, 4, 4, 4, 4, 7, 7, 7, 4, 4, 2, 4, 4, 4, 6, 23, 23, 23, 23, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183848 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546183848 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183848/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183848/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546183848 Building ZINC000546185245 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185245' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185245 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546185245 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185245/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185245 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 534) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/534 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/534' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)[C@@H](c1cccnc1)c1ccc(F)cc1F) `ZINC000546185245.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546185245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185245/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000546185245 none CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)[C@@H](c1cccnc1)c1ccc(F)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', '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, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 7, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 15, 1, 1, 15, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 3, 1, 3, 1, 1, 1, 4, 4, 2, 4, 9, 4, 4, 4, 4, 5, 5, 10, 10, 10, 10, 10, 5, 9, 9, 7, 9, 9, 9, 9, 6, 6, 6, 6, 6, 4, 4, 9, 9, 9, 4, 10, 10, 10, 10, 9, 9, 9] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 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: 79 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185245 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185245/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185245 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 535) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/535 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/535' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)[C@@H](c1cccnc1)c1ccc(F)cc1F) `ZINC000546185245.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546185245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185245/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000546185245 none CCN(C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)[C@@H](c1cccnc1)c1ccc(F)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', '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, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 7, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 15, 1, 1, 15, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 3, 1, 3, 1, 1, 1, 4, 4, 2, 4, 9, 4, 4, 4, 4, 5, 5, 9, 9, 9, 9, 9, 5, 10, 10, 8, 10, 10, 10, 10, 6, 6, 6, 6, 6, 4, 4, 9, 9, 9, 4, 9, 9, 9, 9, 10, 10, 10] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 78 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185245 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546185245 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185245/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185245/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185245 Building ZINC000546185245 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185245' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185245 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546185245 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185245/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185245 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 534) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/534: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)[C@@H](c1cccnc1)c1ccc(F)cc1F) `ZINC000546185245.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546185245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185245/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000546185245 none CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)[C@@H](c1cccnc1)c1ccc(F)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', '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, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 7, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 15, 1, 1, 15, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 3, 1, 3, 1, 1, 1, 4, 4, 2, 4, 9, 4, 4, 4, 4, 5, 5, 10, 10, 10, 10, 10, 5, 9, 9, 7, 9, 9, 9, 9, 6, 6, 6, 6, 6, 4, 4, 9, 9, 9, 4, 10, 10, 10, 10, 9, 9, 9] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 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: 79 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185245 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185245/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185245 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 535) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/535: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)[C@@H](c1cccnc1)c1ccc(F)cc1F) `ZINC000546185245.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546185245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185245/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000546185245 none CCN(C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)[C@@H](c1cccnc1)c1ccc(F)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', '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, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 7, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 15, 1, 1, 15, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 3, 1, 3, 1, 1, 1, 4, 4, 2, 4, 9, 4, 4, 4, 4, 5, 5, 9, 9, 9, 9, 9, 5, 10, 10, 8, 10, 10, 10, 10, 6, 6, 6, 6, 6, 4, 4, 9, 9, 9, 4, 9, 9, 9, 9, 10, 10, 10] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 78 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185245 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546185245 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185245/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185245/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185245 Building ZINC000546185246 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185246' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185246 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546185246 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185246/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185246 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 536) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/536 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/536' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)[C@H](c1cccnc1)c1ccc(F)cc1F) `ZINC000546185246.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546185246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000546185246 none CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)[C@H](c1cccnc1)c1ccc(F)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', '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, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 7, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 15, 1, 1, 15, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 3, 1, 3, 1, 1, 1, 4, 4, 2, 4, 9, 4, 4, 4, 4, 5, 5, 9, 9, 9, 9, 9, 5, 10, 10, 5, 9, 10, 10, 10, 6, 6, 6, 6, 6, 4, 4, 9, 9, 9, 4, 9, 9, 9, 9, 10, 10, 10] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 86 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185246 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185246/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185246 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 537) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/537 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/537' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)[C@H](c1cccnc1)c1ccc(F)cc1F) `ZINC000546185246.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546185246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185246/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000546185246 none CCN(C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)[C@H](c1cccnc1)c1ccc(F)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', '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, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 7, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 15, 1, 1, 15, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 3, 1, 3, 1, 1, 1, 4, 4, 2, 4, 9, 4, 4, 4, 4, 5, 5, 10, 10, 10, 10, 10, 5, 9, 9, 5, 9, 9, 9, 9, 6, 6, 6, 6, 6, 4, 4, 9, 9, 9, 4, 10, 10, 10, 10, 9, 9, 9] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 86 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185246 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546185246 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185246/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185246/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185246 Building ZINC000546185246 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185246' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185246 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546185246 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185246/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185246 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 536) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/536: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)[C@H](c1cccnc1)c1ccc(F)cc1F) `ZINC000546185246.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546185246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000546185246 none CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)[C@H](c1cccnc1)c1ccc(F)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', '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, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 7, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 15, 1, 1, 15, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 3, 1, 3, 1, 1, 1, 4, 4, 2, 4, 9, 4, 4, 4, 4, 5, 5, 9, 9, 9, 9, 9, 5, 10, 10, 5, 9, 10, 10, 10, 6, 6, 6, 6, 6, 4, 4, 9, 9, 9, 4, 9, 9, 9, 9, 10, 10, 10] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 86 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185246 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185246/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185246 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 537) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/537: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)[C@H](c1cccnc1)c1ccc(F)cc1F) `ZINC000546185246.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546185246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185246/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000546185246 none CCN(C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)[C@H](c1cccnc1)c1ccc(F)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', '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, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 7, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 15, 1, 1, 15, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 3, 1, 3, 1, 1, 1, 4, 4, 2, 4, 9, 4, 4, 4, 4, 5, 5, 10, 10, 10, 10, 10, 5, 9, 9, 5, 9, 9, 9, 9, 6, 6, 6, 6, 6, 4, 4, 9, 9, 9, 4, 10, 10, 10, 10, 9, 9, 9] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 86 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185246 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546185246 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185246/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185246/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185246 Building ZINC000546185822 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185822' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185822 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546185822 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185822/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185822 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 538) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/538 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/538' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)Nc1nc2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)cc2s1) `ZINC000546185822.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546185822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185822/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000546185822 none CCCC(=O)Nc1nc2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)cc2s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 3, 3, 1, 3, 1, 1, 1, 6, 6, 2, 6, 11, 6, 6, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 3, 6, 6, 11, 11, 11, 6, 16] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185822 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185822/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185822 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 539) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/539 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/539' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)Nc1nc2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)cc2s1) `ZINC000546185822.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546185822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185822/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000546185822 none CCCC(=O)Nc1nc2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)cc2s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 3, 3, 1, 3, 1, 1, 1, 6, 6, 2, 6, 11, 6, 6, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 3, 6, 6, 11, 11, 11, 6, 16] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185822 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546185822 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185822/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185822/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185822 Building ZINC000546185822 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185822' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185822 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546185822 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185822/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185822 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 538) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/538: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)Nc1nc2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)cc2s1) `ZINC000546185822.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546185822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185822/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000546185822 none CCCC(=O)Nc1nc2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)cc2s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 3, 3, 1, 3, 1, 1, 1, 6, 6, 2, 6, 11, 6, 6, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 3, 6, 6, 11, 11, 11, 6, 16] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185822 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185822/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185822 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 539) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/539: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)Nc1nc2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)cc2s1) `ZINC000546185822.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546185822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185822/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000546185822 none CCCC(=O)Nc1nc2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)cc2s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 3, 3, 1, 3, 1, 1, 1, 6, 6, 2, 6, 11, 6, 6, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 3, 6, 6, 11, 11, 11, 6, 16] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185822 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546185822 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185822/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185822/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546185822 Building ZINC000546187192 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187192' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187192 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546187192 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187192/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187192 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 540) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/540 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/540' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cccc(C[S@@](=O)C3CCCCC3)c2)cc1Cl) `ZINC000546187192.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546187192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000546187192 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cccc(C[S@@](=O)C3CCCCC3)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 5, 5, 5, 5, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 7, 7, 2, 7, 7, 10, 17, 20, 23, 23, 23, 23, 23, 7, 6, 6, 6, 12, 12, 12, 6, 6, 2, 7, 7, 2, 10, 10, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 7, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187192 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187192/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187192 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 541) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/541 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/541' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cccc(C[S@@](=O)C3CCCCC3)c2)cc1Cl) `ZINC000546187192.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546187192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187192/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000546187192 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cccc(C[S@@](=O)C3CCCCC3)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 5, 5, 5, 5, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 11, 18, 21, 23, 23, 23, 23, 23, 9, 6, 6, 6, 10, 10, 10, 6, 6, 3, 9, 9, 9, 11, 11, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187192 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546187192 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187192/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187192/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187192 Building ZINC000546187192 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187192' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187192 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546187192 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187192/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187192 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 540) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/540: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cccc(C[S@@](=O)C3CCCCC3)c2)cc1Cl) `ZINC000546187192.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546187192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000546187192 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cccc(C[S@@](=O)C3CCCCC3)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 5, 5, 5, 5, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 7, 7, 2, 7, 7, 10, 17, 20, 23, 23, 23, 23, 23, 7, 6, 6, 6, 12, 12, 12, 6, 6, 2, 7, 7, 2, 10, 10, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 7, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187192 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187192/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187192 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 541) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/541: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cccc(C[S@@](=O)C3CCCCC3)c2)cc1Cl) `ZINC000546187192.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546187192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187192/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000546187192 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cccc(C[S@@](=O)C3CCCCC3)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 5, 5, 5, 5, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 11, 18, 21, 23, 23, 23, 23, 23, 9, 6, 6, 6, 10, 10, 10, 6, 6, 3, 9, 9, 9, 11, 11, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187192 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546187192 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187192/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187192/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187192 Building ZINC000546187193 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187193' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187193 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546187193 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187193/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187193 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 542) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/542 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/542' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cccc(C[S@](=O)C3CCCCC3)c2)cc1Cl) `ZINC000546187193.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546187193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187193/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000546187193 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cccc(C[S@](=O)C3CCCCC3)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 5, 5, 5, 5, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 12, 18, 21, 24, 24, 24, 24, 24, 9, 6, 6, 6, 11, 11, 11, 6, 6, 3, 9, 9, 9, 12, 12, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 9, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187193 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187193/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187193 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 543) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/543 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/543' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cccc(C[S@](=O)C3CCCCC3)c2)cc1Cl) `ZINC000546187193.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546187193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187193/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000546187193 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cccc(C[S@](=O)C3CCCCC3)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 5, 5, 5, 5, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 10, 16, 20, 23, 23, 23, 23, 23, 7, 6, 6, 6, 12, 12, 12, 6, 6, 2, 7, 7, 7, 10, 10, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 7, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187193 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546187193 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187193/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187193/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187193 Building ZINC000546187193 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187193' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187193 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546187193 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187193/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187193 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 542) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/542: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cccc(C[S@](=O)C3CCCCC3)c2)cc1Cl) `ZINC000546187193.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546187193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187193/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000546187193 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cccc(C[S@](=O)C3CCCCC3)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 5, 5, 5, 5, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 12, 18, 21, 24, 24, 24, 24, 24, 9, 6, 6, 6, 11, 11, 11, 6, 6, 3, 9, 9, 9, 12, 12, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 9, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187193 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187193/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187193 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 543) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/543: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cccc(C[S@](=O)C3CCCCC3)c2)cc1Cl) `ZINC000546187193.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546187193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187193/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000546187193 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cccc(C[S@](=O)C3CCCCC3)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 5, 5, 5, 5, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 10, 16, 20, 23, 23, 23, 23, 23, 7, 6, 6, 6, 12, 12, 12, 6, 6, 2, 7, 7, 7, 10, 10, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 7, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187193 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546187193 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187193/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187193/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187193 Building ZINC000546187195 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187195' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187195 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546187195 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187195/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187195 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 544) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/544 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/544' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Cl)c(C(=O)NC3CCCCC3)c2)cc1Cl) `ZINC000546187195.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546187195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187195/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000546187195 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Cl)c(C(=O)NC3CCCCC3)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 9, 9, 13, 27, 27, 27, 27, 27, 6, 4, 4, 4, 7, 7, 7, 4, 4, 2, 6, 6, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 6, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187195 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187195/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187195 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 545) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/545 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/545' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(Cl)c(C(=O)NC3CCCCC3)c2)cc1Cl) `ZINC000546187195.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546187195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187195/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000546187195 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(Cl)c(C(=O)NC3CCCCC3)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 10, 10, 15, 28, 28, 28, 28, 28, 6, 4, 4, 4, 8, 8, 8, 4, 4, 2, 6, 6, 10, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 6, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187195 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546187195 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187195/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187195/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187195 Building ZINC000546187195 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187195' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187195 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546187195 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187195/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187195 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 544) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/544: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Cl)c(C(=O)NC3CCCCC3)c2)cc1Cl) `ZINC000546187195.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546187195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187195/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000546187195 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Cl)c(C(=O)NC3CCCCC3)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 9, 9, 13, 27, 27, 27, 27, 27, 6, 4, 4, 4, 7, 7, 7, 4, 4, 2, 6, 6, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 6, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187195 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187195/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187195 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 545) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/545: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(Cl)c(C(=O)NC3CCCCC3)c2)cc1Cl) `ZINC000546187195.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546187195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187195/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000546187195 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(Cl)c(C(=O)NC3CCCCC3)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 10, 10, 15, 28, 28, 28, 28, 28, 6, 4, 4, 4, 8, 8, 8, 4, 4, 2, 6, 6, 10, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 6, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187195 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546187195 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187195/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187195/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187195 Building ZINC000546187218 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187218' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187218 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546187218 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187218/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187218 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 546) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/546 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/546' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(C)CCCCCc2cc(c3ccccc3)n[nH]2)cc1Cl) `ZINC000546187218.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546187218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000546187218 none COc1ccc([C@]([O-])([SiH3])C(=O)N(C)CCCCCc2cc(c3ccccc3)n[nH]2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 6, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 3, 3, 8, 11, 11, 11, 12, 19, 19, 19, 33, 33, 19, 33, 33, 19, 19, 19, 4, 4, 4, 7, 7, 7, 4, 4, 3, 3, 3, 8, 8, 11, 11, 11, 11, 11, 11, 12, 12, 19, 33, 33, 29, 33, 33, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187218 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187218/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187218 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 547) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/547 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/547' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)CCCCCc2cc(c3ccccc3)n[nH]2)cc1Cl) `ZINC000546187218.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546187218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187218/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000546187218 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)CCCCCc2cc(c3ccccc3)n[nH]2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 6, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 3, 3, 8, 11, 11, 11, 12, 22, 22, 22, 35, 35, 29, 35, 35, 22, 22, 22, 4, 4, 4, 7, 7, 7, 4, 4, 3, 3, 3, 8, 8, 11, 11, 11, 11, 11, 11, 12, 12, 22, 35, 35, 30, 35, 35, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187218 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546187218 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187218/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187218/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187218 Building ZINC000546187218 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187218' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187218 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546187218 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187218/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187218 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 546) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/546: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(C)CCCCCc2cc(c3ccccc3)n[nH]2)cc1Cl) `ZINC000546187218.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546187218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000546187218 none COc1ccc([C@]([O-])([SiH3])C(=O)N(C)CCCCCc2cc(c3ccccc3)n[nH]2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 6, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 3, 3, 8, 11, 11, 11, 12, 19, 19, 19, 33, 33, 19, 33, 33, 19, 19, 19, 4, 4, 4, 7, 7, 7, 4, 4, 3, 3, 3, 8, 8, 11, 11, 11, 11, 11, 11, 12, 12, 19, 33, 33, 29, 33, 33, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187218 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187218/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187218 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 547) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/547: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)CCCCCc2cc(c3ccccc3)n[nH]2)cc1Cl) `ZINC000546187218.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546187218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187218/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000546187218 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)CCCCCc2cc(c3ccccc3)n[nH]2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 6, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 3, 3, 8, 11, 11, 11, 12, 22, 22, 22, 35, 35, 29, 35, 35, 22, 22, 22, 4, 4, 4, 7, 7, 7, 4, 4, 3, 3, 3, 8, 8, 11, 11, 11, 11, 11, 11, 12, 12, 22, 35, 35, 30, 35, 35, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187218 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546187218 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187218/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187218/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546187218 Building ZINC000546191577 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546191577' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546191577 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546191577 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546191577/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546191577 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 548) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/548 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/548' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)c1ccc(Oc2ccc(C(F)(F)F)cn2)cc1) `ZINC000546191577.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546191577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546191577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000546191577 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)c1ccc(Oc2ccc(C(F)(F)F)cn2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 6, 6, 4, 6, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 50, 50, 50, 6, 6] 50 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546191577 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546191577/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546191577 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 549) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/549 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/549' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)c1ccc(Oc2ccc(C(F)(F)F)cn2)cc1) `ZINC000546191577.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546191577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546191577/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000546191577 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)c1ccc(Oc2ccc(C(F)(F)F)cn2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 5, 5, 2, 2, 20, 49, 49, 49, 49, 49, 49, 49, 49, 49, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 49, 49, 49, 5, 5] 50 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546191577 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546191577 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546191577/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546191577/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546191577 Building ZINC000546191577 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546191577' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546191577 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546191577 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546191577/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546191577 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 548) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/548: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)c1ccc(Oc2ccc(C(F)(F)F)cn2)cc1) `ZINC000546191577.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546191577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546191577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000546191577 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)c1ccc(Oc2ccc(C(F)(F)F)cn2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 6, 6, 4, 6, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 50, 50, 50, 6, 6] 50 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546191577 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546191577/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546191577 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 549) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/549: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)c1ccc(Oc2ccc(C(F)(F)F)cn2)cc1) `ZINC000546191577.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546191577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546191577/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000546191577 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)c1ccc(Oc2ccc(C(F)(F)F)cn2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 5, 5, 2, 2, 20, 49, 49, 49, 49, 49, 49, 49, 49, 49, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 49, 49, 49, 5, 5] 50 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546191577 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546191577 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546191577/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546191577/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546191577 Building ZINC000469899371 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469899371' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469899371 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000469899371 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469899371/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469899371 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 550) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/550 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/550' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)nc2)cc1Cl) `ZINC000469899371.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000469899371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469899371/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000469899371 none COc1ccc(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)nc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 8, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 13, 13, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 4, 4, 3, 4, 8, 4, 4, 4, 4, 4, 13, 13, 13, 25, 25, 25, 13, 13, 4, 4, 2, 4, 4, 8, 8, 8, 4, 4, 13] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469899371 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469899371/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469899371 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 551) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/551 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/551' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)nc2)cc1Cl) `ZINC000469899371.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000469899371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469899371/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000469899371 none COc1ccc(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)nc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 8, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 14, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 8, 4, 4, 4, 4, 4, 14, 14, 14, 26, 26, 26, 14, 14, 4, 4, 2, 4, 4, 8, 8, 8, 4, 4, 14] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469899371 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000469899371 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469899371/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469899371/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469899371 Building ZINC000469899371 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469899371' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469899371 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000469899371 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469899371/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469899371 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 550) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/550: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)nc2)cc1Cl) `ZINC000469899371.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000469899371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469899371/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000469899371 none COc1ccc(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)nc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 8, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 13, 13, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 4, 4, 3, 4, 8, 4, 4, 4, 4, 4, 13, 13, 13, 25, 25, 25, 13, 13, 4, 4, 2, 4, 4, 8, 8, 8, 4, 4, 13] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469899371 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469899371/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469899371 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 551) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/551: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)nc2)cc1Cl) `ZINC000469899371.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000469899371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469899371/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000469899371 none COc1ccc(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)nc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 8, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 14, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 8, 4, 4, 4, 4, 4, 14, 14, 14, 26, 26, 26, 14, 14, 4, 4, 2, 4, 4, 8, 8, 8, 4, 4, 14] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469899371 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000469899371 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469899371/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469899371/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000469899371 Building ZINC000546813979 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546813979' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546813979 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546813979 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546813979/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546813979 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 552) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/552 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/552' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C(=O)c2c(NC(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)sc3c2CCOC3)cc1) `ZINC000546813979.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546813979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546813979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000546813979 none Cc1ccc(C(=O)c2c(NC(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)sc3c2CCOC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 14, 1, 1, 5, 5, 12, 5, 1, 1, 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, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 47, 30, 47, 30, 7, 7, 1, 7, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 30, 30, 30, 30, 30, 30, 30, 47, 47, 47, 47, 47, 47, 47, 7, 3, 3, 3, 3, 3, 3, 30, 30, 30, 30, 30, 30, 47, 47] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 106 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546813979 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546813979/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546813979 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 553) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/553 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/553' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C(=O)c2c(NC(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)sc3c2CCOC3)cc1) `ZINC000546813979.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546813979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546813979/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000546813979 none Cc1ccc(C(=O)c2c(NC(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)sc3c2CCOC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 14, 1, 1, 5, 5, 12, 5, 1, 1, 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, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 46, 29, 46, 29, 7, 7, 1, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 29, 29, 29, 29, 29, 29, 29, 47, 47, 47, 47, 47, 47, 47, 7, 4, 4, 4, 4, 4, 4, 29, 29, 29, 29, 29, 29, 47, 47] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546813979 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546813979 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546813979/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546813979/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546813979 Building ZINC000546813979 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546813979' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546813979 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546813979 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546813979/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546813979 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 552) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/552: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C(=O)c2c(NC(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)sc3c2CCOC3)cc1) `ZINC000546813979.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546813979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546813979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000546813979 none Cc1ccc(C(=O)c2c(NC(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)sc3c2CCOC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 14, 1, 1, 5, 5, 12, 5, 1, 1, 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, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 47, 30, 47, 30, 7, 7, 1, 7, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 30, 30, 30, 30, 30, 30, 30, 47, 47, 47, 47, 47, 47, 47, 7, 3, 3, 3, 3, 3, 3, 30, 30, 30, 30, 30, 30, 47, 47] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 106 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546813979 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546813979/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546813979 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 553) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/553: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C(=O)c2c(NC(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)sc3c2CCOC3)cc1) `ZINC000546813979.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546813979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546813979/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000546813979 none Cc1ccc(C(=O)c2c(NC(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)sc3c2CCOC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 14, 1, 1, 5, 5, 12, 5, 1, 1, 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, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 46, 29, 46, 29, 7, 7, 1, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 29, 29, 29, 29, 29, 29, 29, 47, 47, 47, 47, 47, 47, 47, 7, 4, 4, 4, 4, 4, 4, 29, 29, 29, 29, 29, 29, 47, 47] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546813979 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546813979 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546813979/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546813979/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546813979 Building ZINC000546865489 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546865489' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546865489 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546865489 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546865489/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546865489 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 554) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/554 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/554' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2cccc(NC(=O)c3ccccc3)c2)cc1Cl) `ZINC000546865489.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546865489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546865489/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000546865489 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2cccc(NC(=O)c3ccccc3)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 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, 3, 7, 7, 7, 9, 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: [11, 6, 2, 6, 6, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 10, 10, 10, 10, 10, 13, 13, 13, 22, 22, 22, 22, 22, 10, 6, 6, 6, 11, 11, 11, 6, 6, 2, 4, 4, 4, 10, 10, 10, 13, 22, 22, 22, 22, 22, 10, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 85 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546865489 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546865489/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546865489 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 555) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/555 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/555' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2cccc(NC(=O)c3ccccc3)c2)cc1Cl) `ZINC000546865489.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546865489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546865489/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000546865489 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2cccc(NC(=O)c3ccccc3)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 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, 3, 7, 7, 7, 9, 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: [9, 5, 2, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 10, 10, 10, 10, 10, 14, 14, 14, 24, 24, 24, 24, 24, 10, 5, 5, 5, 9, 9, 9, 5, 5, 2, 4, 4, 4, 10, 10, 10, 14, 24, 24, 24, 24, 24, 10, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 88 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546865489 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546865489 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546865489/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546865489/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546865489 Building ZINC000546865489 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546865489' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546865489 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546865489 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546865489/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546865489 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 554) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/554: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2cccc(NC(=O)c3ccccc3)c2)cc1Cl) `ZINC000546865489.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546865489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546865489/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000546865489 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2cccc(NC(=O)c3ccccc3)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 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, 3, 7, 7, 7, 9, 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: [11, 6, 2, 6, 6, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 10, 10, 10, 10, 10, 13, 13, 13, 22, 22, 22, 22, 22, 10, 6, 6, 6, 11, 11, 11, 6, 6, 2, 4, 4, 4, 10, 10, 10, 13, 22, 22, 22, 22, 22, 10, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 85 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546865489 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546865489/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546865489 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 555) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/555: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2cccc(NC(=O)c3ccccc3)c2)cc1Cl) `ZINC000546865489.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546865489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546865489/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000546865489 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2cccc(NC(=O)c3ccccc3)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 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, 3, 7, 7, 7, 9, 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: [9, 5, 2, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 10, 10, 10, 10, 10, 14, 14, 14, 24, 24, 24, 24, 24, 10, 5, 5, 5, 9, 9, 9, 5, 5, 2, 4, 4, 4, 10, 10, 10, 14, 24, 24, 24, 24, 24, 10, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 88 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546865489 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546865489 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546865489/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546865489/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546865489 Building ZINC000546865490 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546865490' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546865490 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546865490 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546865490/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546865490 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 556) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/556 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/556' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2cccc(NC(=O)c3ccccc3)c2)cc1Cl) `ZINC000546865490.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546865490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546865490/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000546865490 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2cccc(NC(=O)c3ccccc3)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 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, 3, 7, 7, 7, 9, 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: [9, 5, 2, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 10, 10, 10, 10, 10, 14, 14, 14, 24, 24, 24, 24, 24, 10, 5, 5, 5, 9, 9, 9, 5, 5, 2, 4, 4, 4, 10, 10, 10, 14, 24, 24, 24, 24, 24, 10, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 88 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546865490 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546865490/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546865490 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 557) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/557 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/557' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2cccc(NC(=O)c3ccccc3)c2)cc1Cl) `ZINC000546865490.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546865490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546865490/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000546865490 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2cccc(NC(=O)c3ccccc3)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 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, 3, 7, 7, 7, 9, 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: [12, 6, 2, 6, 6, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 10, 10, 10, 10, 10, 13, 13, 13, 25, 25, 13, 25, 25, 10, 6, 6, 6, 12, 12, 12, 6, 6, 2, 4, 4, 4, 10, 10, 10, 13, 25, 25, 25, 25, 25, 10, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 152 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546865490 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546865490 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546865490/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546865490/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546865490 Building ZINC000546865490 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546865490' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546865490 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546865490 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546865490/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546865490 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 556) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/556: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2cccc(NC(=O)c3ccccc3)c2)cc1Cl) `ZINC000546865490.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546865490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546865490/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000546865490 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2cccc(NC(=O)c3ccccc3)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 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, 3, 7, 7, 7, 9, 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: [9, 5, 2, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 10, 10, 10, 10, 10, 14, 14, 14, 24, 24, 24, 24, 24, 10, 5, 5, 5, 9, 9, 9, 5, 5, 2, 4, 4, 4, 10, 10, 10, 14, 24, 24, 24, 24, 24, 10, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 88 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546865490 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546865490/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546865490 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 557) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/557: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2cccc(NC(=O)c3ccccc3)c2)cc1Cl) `ZINC000546865490.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546865490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546865490/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000546865490 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2cccc(NC(=O)c3ccccc3)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 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, 3, 7, 7, 7, 9, 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: [12, 6, 2, 6, 6, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 10, 10, 10, 10, 10, 13, 13, 13, 25, 25, 13, 25, 25, 10, 6, 6, 6, 12, 12, 12, 6, 6, 2, 4, 4, 4, 10, 10, 10, 13, 25, 25, 25, 25, 25, 10, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 152 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546865490 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546865490 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546865490/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546865490/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546865490 Building ZINC000546867795 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546867795' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546867795 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546867795 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546867795/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546867795 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 558) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/558 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/558' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Cl)cc2NC(=O)c2ccco2)cc1Cl) `ZINC000546867795.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546867795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546867795/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000546867795 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Cl)cc2NC(=O)c2ccco2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 1, 1, 1, 1, 12, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 14, 14, 14, 17, 17, 17, 17, 6, 6, 6, 12, 12, 12, 6, 6, 3, 8, 8, 8, 14, 17, 17, 17, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546867795 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546867795/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546867795 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 559) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/559 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/559' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(Cl)cc2NC(=O)c2ccco2)cc1Cl) `ZINC000546867795.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546867795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546867795/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000546867795 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(Cl)cc2NC(=O)c2ccco2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 1, 1, 1, 1, 12, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 8, 8, 5, 8, 8, 8, 8, 14, 14, 14, 18, 18, 18, 18, 6, 6, 6, 12, 12, 12, 6, 6, 3, 8, 8, 8, 14, 18, 18, 18, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546867795 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546867795 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546867795/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546867795/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546867795 Building ZINC000546867795 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546867795' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546867795 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546867795 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546867795/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546867795 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 558) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/558: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Cl)cc2NC(=O)c2ccco2)cc1Cl) `ZINC000546867795.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546867795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546867795/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000546867795 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Cl)cc2NC(=O)c2ccco2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 1, 1, 1, 1, 12, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 14, 14, 14, 17, 17, 17, 17, 6, 6, 6, 12, 12, 12, 6, 6, 3, 8, 8, 8, 14, 17, 17, 17, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546867795 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546867795/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546867795 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 559) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/559: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(Cl)cc2NC(=O)c2ccco2)cc1Cl) `ZINC000546867795.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546867795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546867795/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000546867795 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(Cl)cc2NC(=O)c2ccco2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 1, 1, 1, 1, 12, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 8, 8, 5, 8, 8, 8, 8, 14, 14, 14, 18, 18, 18, 18, 6, 6, 6, 12, 12, 12, 6, 6, 3, 8, 8, 8, 14, 18, 18, 18, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546867795 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546867795 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546867795/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546867795/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546867795 Building ZINC000546876354 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546876354' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546876354 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546876354 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546876354/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546876354 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 560) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/560 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/560' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CC(F)(F)F)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000546876354.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546876354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546876354/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000546876354 none CC[C@H](CC(F)(F)F)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'F', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', '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, 15, 15, 15, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 6, 2, 6, 6, 7, 7, 7, 7, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 20, 20, 4, 20, 20, 20, 20, 20, 20, 4, 4, 7, 7, 7, 7, 7, 7, 7, 2, 4, 4, 4, 20, 20, 4, 20, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 93 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546876354 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546876354/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546876354 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 561) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/561 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/561' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CC(F)(F)F)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000546876354.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546876354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546876354/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000546876354 none CC[C@H](CC(F)(F)F)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'F', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', '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, 15, 15, 15, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 2, 7, 7, 9, 9, 9, 9, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 18, 18, 4, 18, 18, 18, 18, 18, 18, 4, 4, 8, 8, 8, 8, 8, 9, 9, 2, 4, 4, 4, 18, 18, 4, 18, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 101 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546876354 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546876354 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546876354/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546876354/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546876354 Building ZINC000546876354 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546876354' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546876354 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546876354 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546876354/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546876354 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 560) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/560: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CC(F)(F)F)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000546876354.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546876354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546876354/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000546876354 none CC[C@H](CC(F)(F)F)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'F', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', '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, 15, 15, 15, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 6, 2, 6, 6, 7, 7, 7, 7, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 20, 20, 4, 20, 20, 20, 20, 20, 20, 4, 4, 7, 7, 7, 7, 7, 7, 7, 2, 4, 4, 4, 20, 20, 4, 20, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 93 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546876354 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546876354/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546876354 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 561) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/561: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CC(F)(F)F)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000546876354.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546876354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546876354/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000546876354 none CC[C@H](CC(F)(F)F)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'F', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', '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, 15, 15, 15, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 2, 7, 7, 9, 9, 9, 9, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 18, 18, 4, 18, 18, 18, 18, 18, 18, 4, 4, 8, 8, 8, 8, 8, 9, 9, 2, 4, 4, 4, 18, 18, 4, 18, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 101 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546876354 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546876354 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546876354/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546876354/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546876354 Building ZINC000546876355 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546876355' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546876355 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546876355 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546876355/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546876355 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 562) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/562 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/562' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CC(F)(F)F)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000546876355.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546876355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546876355/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000546876355 none CC[C@@H](CC(F)(F)F)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'F', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', '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, 15, 15, 15, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 11, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 20, 20, 4, 20, 20, 20, 20, 20, 20, 4, 4, 9, 9, 9, 9, 9, 11, 11, 2, 4, 4, 4, 20, 20, 8, 20, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 127 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546876355 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546876355/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546876355 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 563) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/563 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/563' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CC(F)(F)F)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000546876355.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546876355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546876355/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000546876355 none CC[C@@H](CC(F)(F)F)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'F', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', '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, 15, 15, 15, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 21, 21, 4, 21, 21, 21, 21, 21, 21, 4, 4, 9, 9, 9, 9, 9, 7, 7, 2, 4, 4, 4, 21, 21, 4, 21, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 100 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546876355 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546876355 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546876355/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546876355/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546876355 Building ZINC000546876355 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546876355' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546876355 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546876355 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546876355/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546876355 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 562) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/562: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CC(F)(F)F)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000546876355.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546876355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546876355/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000546876355 none CC[C@@H](CC(F)(F)F)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'F', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', '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, 15, 15, 15, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 11, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 20, 20, 4, 20, 20, 20, 20, 20, 20, 4, 4, 9, 9, 9, 9, 9, 11, 11, 2, 4, 4, 4, 20, 20, 8, 20, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 127 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546876355 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546876355/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546876355 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 563) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/563: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CC(F)(F)F)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000546876355.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546876355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546876355/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000546876355 none CC[C@@H](CC(F)(F)F)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'F', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', '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, 15, 15, 15, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 21, 21, 4, 21, 21, 21, 21, 21, 21, 4, 4, 9, 9, 9, 9, 9, 7, 7, 2, 4, 4, 4, 21, 21, 4, 21, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 100 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546876355 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546876355 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546876355/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546876355/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546876355 Building ZINC000546888514 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546888514' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546888514 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546888514 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546888514/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546888514 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 564) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/564 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/564' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOc1c(Cl)cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)cc1Cl) `ZINC000546888514.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546888514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546888514/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000546888514 none COCCOc1c(Cl)cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 22, 9, 4, 2, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 8, 4, 4, 4, 5, 5, 5, 29, 29, 29, 22, 22, 22, 22, 5, 2, 4, 4, 8, 8, 8, 4, 5] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546888514 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546888514/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546888514 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 565) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/565 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/565' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOc1c(Cl)cc(NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)cc1Cl) `ZINC000546888514.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546888514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546888514/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000546888514 none COCCOc1c(Cl)cc(NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 21, 21, 8, 2, 2, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 8, 4, 4, 4, 4, 4, 4, 28, 28, 28, 21, 21, 21, 21, 4, 2, 4, 4, 8, 8, 8, 4, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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/129831/xbf-8058088.32/working/building/ZINC000546888514 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546888514 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546888514/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546888514/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546888514 Building ZINC000546888514 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546888514' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546888514 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546888514 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546888514/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546888514 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 564) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/564: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOc1c(Cl)cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)cc1Cl) `ZINC000546888514.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546888514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546888514/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000546888514 none COCCOc1c(Cl)cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 22, 9, 4, 2, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 8, 4, 4, 4, 5, 5, 5, 29, 29, 29, 22, 22, 22, 22, 5, 2, 4, 4, 8, 8, 8, 4, 5] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546888514 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546888514/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546888514 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 565) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/565: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOc1c(Cl)cc(NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)cc1Cl) `ZINC000546888514.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546888514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546888514/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000546888514 none COCCOc1c(Cl)cc(NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 21, 21, 8, 2, 2, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 8, 4, 4, 4, 4, 4, 4, 28, 28, 28, 21, 21, 21, 21, 4, 2, 4, 4, 8, 8, 8, 4, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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/129831/xbf-8058088.32/working/building/ZINC000546888514 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546888514 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546888514/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546888514/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546888514 Building ZINC000546890826 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546890826' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546890826 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546890826 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546890826/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546890826 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 566) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/566 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/566' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccc(C(F)(F)F)cn2)c(F)c1) `ZINC000546890826.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546890826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546890826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000546890826 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccc(C(F)(F)F)cn2)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 8, 8, 50, 50, 50, 8] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546890826 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546890826/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546890826 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 567) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/567 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/567' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccc(C(F)(F)F)cn2)c(F)c1) `ZINC000546890826.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546890826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546890826/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000546890826 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccc(C(F)(F)F)cn2)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 8, 8, 50, 50, 50, 8] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546890826 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546890826 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546890826/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546890826/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546890826 Building ZINC000546890826 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546890826' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546890826 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546890826 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546890826/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546890826 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 566) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/566: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccc(C(F)(F)F)cn2)c(F)c1) `ZINC000546890826.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546890826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546890826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000546890826 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccc(C(F)(F)F)cn2)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 8, 8, 50, 50, 50, 8] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546890826 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546890826/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546890826 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 567) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/567: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccc(C(F)(F)F)cn2)c(F)c1) `ZINC000546890826.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546890826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546890826/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000546890826 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ccc(Oc2ccc(C(F)(F)F)cn2)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 8, 8, 50, 50, 50, 8] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546890826 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546890826 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546890826/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546890826/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546890826 Building ZINC000546890038 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546890038' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546890038 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546890038 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546890038/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546890038 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 568) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/568 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/568' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCc2c(NC(=O)Nc3ccccc3F)cccc21) `ZINC000546890038.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546890038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546890038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000546890038 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCc2c(NC(=O)Nc3ccccc3F)cccc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 2, 4, 6, 6, 6, 6, 6, 6, 6, 23, 23, 23, 23, 50, 50, 23, 50, 50, 50, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6, 6, 23, 23, 50, 50, 49, 50, 6, 6, 6] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546890038 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546890038/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546890038 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 569) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/569 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/569' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCc2c(NC(=O)Nc3ccccc3F)cccc21) `ZINC000546890038.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546890038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546890038/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000546890038 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCc2c(NC(=O)Nc3ccccc3F)cccc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 2, 4, 6, 6, 6, 6, 6, 6, 6, 23, 23, 23, 23, 50, 50, 44, 50, 50, 50, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6, 6, 23, 23, 50, 50, 50, 50, 6, 6, 6] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546890038 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546890038 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546890038/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546890038/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546890038 Building ZINC000546890038 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546890038' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546890038 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546890038 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546890038/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546890038 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 568) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/568: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCc2c(NC(=O)Nc3ccccc3F)cccc21) `ZINC000546890038.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546890038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546890038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000546890038 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCc2c(NC(=O)Nc3ccccc3F)cccc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 2, 4, 6, 6, 6, 6, 6, 6, 6, 23, 23, 23, 23, 50, 50, 23, 50, 50, 50, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6, 6, 23, 23, 50, 50, 49, 50, 6, 6, 6] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546890038 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546890038/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546890038 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 569) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/569: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCc2c(NC(=O)Nc3ccccc3F)cccc21) `ZINC000546890038.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546890038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546890038/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000546890038 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCc2c(NC(=O)Nc3ccccc3F)cccc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 2, 4, 6, 6, 6, 6, 6, 6, 6, 23, 23, 23, 23, 50, 50, 44, 50, 50, 50, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6, 6, 23, 23, 50, 50, 50, 50, 6, 6, 6] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546890038 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546890038 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546890038/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546890038/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546890038 Building ZINC000546891716 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891716' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891716 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546891716 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891716/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891716 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 570) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/570 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/570' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2nc(c3ccccc3OC(F)F)cs2)cc1Cl) `ZINC000546891716.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546891716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891716/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000546891716 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2nc(c3ccccc3OC(F)F)cs2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.2', 'S.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 14, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 3, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 16, 16, 8, 16, 16, 16, 25, 27, 27, 4, 4, 4, 4, 4, 9, 9, 9, 4, 4, 2, 16, 16, 16, 16, 27, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891716 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891716/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891716 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 571) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/571 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/571' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2nc(c3ccccc3OC(F)F)cs2)cc1Cl) `ZINC000546891716.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546891716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891716/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000546891716 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2nc(c3ccccc3OC(F)F)cs2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.2', 'S.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 14, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 16, 16, 8, 16, 16, 16, 24, 26, 26, 4, 4, 4, 4, 4, 9, 9, 9, 4, 4, 2, 16, 16, 16, 16, 26, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891716 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546891716 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891716/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891716/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891716 Building ZINC000546891716 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891716' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891716 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546891716 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891716/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891716 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 570) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/570: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2nc(c3ccccc3OC(F)F)cs2)cc1Cl) `ZINC000546891716.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546891716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891716/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000546891716 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2nc(c3ccccc3OC(F)F)cs2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.2', 'S.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 14, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 3, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 16, 16, 8, 16, 16, 16, 25, 27, 27, 4, 4, 4, 4, 4, 9, 9, 9, 4, 4, 2, 16, 16, 16, 16, 27, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891716 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891716/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891716 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 571) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/571: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2nc(c3ccccc3OC(F)F)cs2)cc1Cl) `ZINC000546891716.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546891716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891716/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000546891716 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2nc(c3ccccc3OC(F)F)cs2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.2', 'S.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 14, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 16, 16, 8, 16, 16, 16, 24, 26, 26, 4, 4, 4, 4, 4, 9, 9, 9, 4, 4, 2, 16, 16, 16, 16, 26, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891716 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546891716 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891716/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891716/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891716 Building ZINC000546891444 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891444' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891444 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546891444 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891444/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891444 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 572) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/572 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/572' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(OC)c(NC(=O)C3CCCCC3)c2)cc1Cl) `ZINC000546891444.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546891444.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891444/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000546891444 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(OC)c(NC(=O)C3CCCCC3)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 1, 1, 16, 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] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 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: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 6, 2, 2, 4, 4, 7, 18, 18, 18, 18, 18, 2, 2, 2, 2, 4, 4, 4, 2, 2, 1, 2, 2, 6, 6, 6, 4, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 2, 2] 50 rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891444 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891444/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891444 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 573) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/573 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/573' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(OC)c(NC(=O)C3CCCCC3)c2)cc1Cl) `ZINC000546891444.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546891444.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891444/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000546891444 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(OC)c(NC(=O)C3CCCCC3)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 1, 1, 16, 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] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 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: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 6, 2, 2, 4, 4, 7, 20, 20, 20, 20, 20, 2, 2, 2, 2, 4, 4, 4, 2, 2, 1, 2, 2, 6, 6, 6, 4, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 2, 2] 50 rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891444 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546891444 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891444/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891444/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891444 Building ZINC000546891444 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891444' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891444 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546891444 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891444/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891444 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 572) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/572: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(OC)c(NC(=O)C3CCCCC3)c2)cc1Cl) `ZINC000546891444.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546891444.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891444/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000546891444 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(OC)c(NC(=O)C3CCCCC3)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 1, 1, 16, 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] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 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: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 6, 2, 2, 4, 4, 7, 18, 18, 18, 18, 18, 2, 2, 2, 2, 4, 4, 4, 2, 2, 1, 2, 2, 6, 6, 6, 4, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 2, 2] 50 rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891444 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891444/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891444 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 573) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/573: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(OC)c(NC(=O)C3CCCCC3)c2)cc1Cl) `ZINC000546891444.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546891444.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891444/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000546891444 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(OC)c(NC(=O)C3CCCCC3)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 1, 1, 16, 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] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 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: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 6, 2, 2, 4, 4, 7, 20, 20, 20, 20, 20, 2, 2, 2, 2, 4, 4, 4, 2, 2, 1, 2, 2, 6, 6, 6, 4, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 2, 2] 50 rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891444 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546891444 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891444/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891444/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891444 Building ZINC000546891058 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891058' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891058 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546891058 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891058/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891058 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 574) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/574 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/574' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1C(=O)N1[C@H](C)CCC[C@@H]1C) `ZINC000546891058.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546891058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000546891058 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1C(=O)N1[C@H](C)CCC[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 14, 21, 34, 34, 45, 45, 45, 45, 45, 45, 45, 45, 45, 5, 5, 5, 5, 5, 5, 5, 6, 14, 14, 14, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891058 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891058/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891058 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 575) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/575 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/575' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1C(=O)N1[C@H](C)CCC[C@@H]1C) `ZINC000546891058.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546891058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891058/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000546891058 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1C(=O)N1[C@H](C)CCC[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 13, 13, 13, 20, 36, 36, 46, 46, 46, 46, 46, 46, 46, 46, 46, 3, 3, 3, 3, 3, 3, 3, 6, 13, 13, 13, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 116 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891058 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546891058 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891058/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891058/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891058 Building ZINC000546891058 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891058' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891058 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546891058 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891058/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891058 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 574) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/574: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1C(=O)N1[C@H](C)CCC[C@@H]1C) `ZINC000546891058.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546891058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000546891058 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1C(=O)N1[C@H](C)CCC[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 14, 21, 34, 34, 45, 45, 45, 45, 45, 45, 45, 45, 45, 5, 5, 5, 5, 5, 5, 5, 6, 14, 14, 14, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891058 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891058/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891058 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 575) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/575: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1C(=O)N1[C@H](C)CCC[C@@H]1C) `ZINC000546891058.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546891058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891058/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000546891058 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1C(=O)N1[C@H](C)CCC[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 13, 13, 13, 20, 36, 36, 46, 46, 46, 46, 46, 46, 46, 46, 46, 3, 3, 3, 3, 3, 3, 3, 6, 13, 13, 13, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 116 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891058 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546891058 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891058/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891058/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891058 Building ZINC000546891059 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891059' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891059 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546891059 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891059/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891059 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 576) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/576 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/576' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1C(=O)N1[C@@H](C)CCC[C@@H]1C) `ZINC000546891059.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546891059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891059/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000546891059 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1C(=O)N1[C@@H](C)CCC[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 13, 13, 13, 18, 35, 35, 43, 43, 43, 43, 43, 43, 43, 43, 43, 5, 5, 5, 5, 5, 5, 5, 6, 13, 13, 13, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891059 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891059/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891059 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 577) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/577 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/577' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1C(=O)N1[C@@H](C)CCC[C@@H]1C) `ZINC000546891059.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546891059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891059/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000546891059 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1C(=O)N1[C@@H](C)CCC[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 10, 10, 10, 16, 37, 37, 46, 46, 46, 46, 46, 46, 46, 46, 46, 6, 6, 6, 5, 5, 5, 5, 5, 10, 10, 10, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891059 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546891059 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891059/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891059/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891059 Building ZINC000546891059 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891059' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891059 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546891059 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891059/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891059 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 576) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/576: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1C(=O)N1[C@@H](C)CCC[C@@H]1C) `ZINC000546891059.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546891059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891059/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000546891059 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1C(=O)N1[C@@H](C)CCC[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 13, 13, 13, 18, 35, 35, 43, 43, 43, 43, 43, 43, 43, 43, 43, 5, 5, 5, 5, 5, 5, 5, 6, 13, 13, 13, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891059 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891059/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891059 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 577) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/577: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1C(=O)N1[C@@H](C)CCC[C@@H]1C) `ZINC000546891059.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546891059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891059/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000546891059 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1C(=O)N1[C@@H](C)CCC[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 10, 10, 10, 16, 37, 37, 46, 46, 46, 46, 46, 46, 46, 46, 46, 6, 6, 6, 5, 5, 5, 5, 5, 10, 10, 10, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891059 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546891059 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891059/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891059/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891059 Building ZINC000546891060 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891060' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891060 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546891060 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891060/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891060 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 578) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/578 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/578' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1C(=O)N1[C@H](C)CCC[C@H]1C) `ZINC000546891060.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546891060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891060/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000546891060 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1C(=O)N1[C@H](C)CCC[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 3, 4, 4, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 13, 13, 13, 25, 41, 41, 46, 46, 46, 46, 46, 46, 46, 46, 46, 4, 4, 4, 4, 4, 4, 4, 6, 13, 13, 13, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891060 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891060/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891060 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 579) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/579 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/579' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1C(=O)N1[C@H](C)CCC[C@H]1C) `ZINC000546891060.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546891060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891060/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000546891060 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1C(=O)N1[C@H](C)CCC[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 12, 25, 40, 40, 47, 47, 47, 47, 47, 47, 47, 47, 47, 3, 3, 3, 3, 3, 3, 3, 6, 12, 12, 12, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891060 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546891060 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891060/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891060/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891060 Building ZINC000546891060 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891060' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891060 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546891060 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891060/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891060 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 578) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/578: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1C(=O)N1[C@H](C)CCC[C@H]1C) `ZINC000546891060.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546891060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891060/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000546891060 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1C(=O)N1[C@H](C)CCC[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 3, 4, 4, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 13, 13, 13, 25, 41, 41, 46, 46, 46, 46, 46, 46, 46, 46, 46, 4, 4, 4, 4, 4, 4, 4, 6, 13, 13, 13, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891060 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891060/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891060 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 579) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/579: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1C(=O)N1[C@H](C)CCC[C@H]1C) `ZINC000546891060.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546891060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891060/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000546891060 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1C(=O)N1[C@H](C)CCC[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 12, 25, 40, 40, 47, 47, 47, 47, 47, 47, 47, 47, 47, 3, 3, 3, 3, 3, 3, 3, 6, 12, 12, 12, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891060 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546891060 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891060/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891060/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891060 Building ZINC000546891071 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891071' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891071 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546891071 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891071/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891071 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 580) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/580 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/580' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Sc3nncs3)c(Cl)c2)cc1Cl) `ZINC000546891071.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546891071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000546891071 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Sc3nncs3)c(Cl)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 1, 8, 8, 1, 14, 1, 16, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 20, 31, 31, 31, 31, 7, 7, 7, 4, 4, 4, 7, 7, 7, 4, 4, 2, 7, 7, 31, 7, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891071 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891071/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891071 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 581) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/581 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/581' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(Sc3nncs3)c(Cl)c2)cc1Cl) `ZINC000546891071.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546891071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891071/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000546891071 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(Sc3nncs3)c(Cl)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 1, 8, 8, 1, 14, 1, 16, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 21, 32, 32, 32, 32, 8, 8, 8, 4, 4, 4, 7, 7, 7, 4, 4, 2, 8, 8, 32, 8, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891071 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546891071 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891071/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891071/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891071 Building ZINC000546891071 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891071' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891071 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546891071 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891071/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891071 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 580) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/580: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Sc3nncs3)c(Cl)c2)cc1Cl) `ZINC000546891071.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546891071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000546891071 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Sc3nncs3)c(Cl)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 1, 8, 8, 1, 14, 1, 16, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 20, 31, 31, 31, 31, 7, 7, 7, 4, 4, 4, 7, 7, 7, 4, 4, 2, 7, 7, 31, 7, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891071 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891071/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891071 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 581) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/581: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(Sc3nncs3)c(Cl)c2)cc1Cl) `ZINC000546891071.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546891071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891071/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000546891071 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(Sc3nncs3)c(Cl)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 1, 8, 8, 1, 14, 1, 16, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 21, 32, 32, 32, 32, 8, 8, 8, 4, 4, 4, 7, 7, 7, 4, 4, 2, 8, 8, 32, 8, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891071 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546891071 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891071/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891071/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891071 Building ZINC000546891950 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891950' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891950 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546891950 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891950/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891950 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 582) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/582 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/582' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2nc(C)c([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)s2)cc1) `ZINC000546891950.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546891950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891950/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000546891950 none COc1ccc(c2nc(C)c([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)s2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 22, 22, 10, 10, 10, 10, 10, 5, 3, 5, 5, 3, 1, 3, 1, 1, 1, 6, 6, 2, 6, 13, 6, 6, 6, 10, 22, 22, 22, 22, 22, 22, 22, 10, 10, 10, 5, 5, 5, 3, 6, 6, 13, 13, 13, 6, 22, 22] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 88 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891950 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891950/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891950 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 583) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/583 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/583' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2nc(C)c([C@@H](C)NC(=O)[C@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)s2)cc1) `ZINC000546891950.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546891950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891950/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000546891950 none COc1ccc(c2nc(C)c([C@@H](C)NC(=O)[C@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)s2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 18, 20, 20, 10, 10, 10, 10, 10, 4, 3, 4, 4, 3, 1, 3, 1, 1, 1, 6, 6, 2, 6, 12, 6, 6, 6, 10, 20, 20, 20, 20, 20, 20, 20, 10, 10, 10, 4, 4, 4, 3, 6, 6, 12, 12, 12, 6, 20, 20] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 83 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891950 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546891950 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891950/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891950/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891950 Building ZINC000546891950 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891950' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891950 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546891950 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891950/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891950 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 582) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/582: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2nc(C)c([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)s2)cc1) `ZINC000546891950.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546891950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891950/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000546891950 none COc1ccc(c2nc(C)c([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)s2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 22, 22, 10, 10, 10, 10, 10, 5, 3, 5, 5, 3, 1, 3, 1, 1, 1, 6, 6, 2, 6, 13, 6, 6, 6, 10, 22, 22, 22, 22, 22, 22, 22, 10, 10, 10, 5, 5, 5, 3, 6, 6, 13, 13, 13, 6, 22, 22] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 88 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891950 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891950/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891950 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 583) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/583: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2nc(C)c([C@@H](C)NC(=O)[C@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)s2)cc1) `ZINC000546891950.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546891950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891950/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000546891950 none COc1ccc(c2nc(C)c([C@@H](C)NC(=O)[C@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)s2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 18, 20, 20, 10, 10, 10, 10, 10, 4, 3, 4, 4, 3, 1, 3, 1, 1, 1, 6, 6, 2, 6, 12, 6, 6, 6, 10, 20, 20, 20, 20, 20, 20, 20, 10, 10, 10, 4, 4, 4, 3, 6, 6, 12, 12, 12, 6, 20, 20] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 83 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891950 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546891950 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891950/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891950/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891950 Building ZINC000546891951 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891951' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891951 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546891951 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891951/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891951 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 584) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/584 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/584' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2nc(C)c([C@H](C)NC(=O)[C@@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)s2)cc1) `ZINC000546891951.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546891951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891951/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000546891951 none COc1ccc(c2nc(C)c([C@H](C)NC(=O)[C@@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)s2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 18, 10, 21, 21, 10, 10, 10, 10, 10, 4, 3, 4, 4, 3, 1, 3, 1, 1, 1, 6, 6, 2, 6, 12, 6, 6, 6, 10, 21, 21, 21, 21, 21, 21, 21, 10, 10, 10, 4, 4, 4, 3, 6, 6, 12, 12, 12, 6, 21, 21] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 125 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891951 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891951/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891951 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 585) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/585 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/585' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2nc(C)c([C@H](C)NC(=O)[C@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)s2)cc1) `ZINC000546891951.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546891951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891951/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000546891951 none COc1ccc(c2nc(C)c([C@H](C)NC(=O)[C@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)s2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 20, 18, 22, 22, 10, 10, 10, 10, 10, 5, 3, 5, 5, 3, 1, 3, 1, 1, 1, 6, 6, 2, 6, 13, 6, 6, 6, 10, 22, 22, 22, 22, 22, 22, 22, 10, 10, 10, 5, 5, 5, 3, 6, 6, 13, 13, 13, 6, 22, 22] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 98 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891951 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546891951 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891951/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891951/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891951 Building ZINC000546891951 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891951' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891951 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546891951 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891951/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891951 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 584) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/584: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2nc(C)c([C@H](C)NC(=O)[C@@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)s2)cc1) `ZINC000546891951.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546891951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891951/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000546891951 none COc1ccc(c2nc(C)c([C@H](C)NC(=O)[C@@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)s2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 18, 10, 21, 21, 10, 10, 10, 10, 10, 4, 3, 4, 4, 3, 1, 3, 1, 1, 1, 6, 6, 2, 6, 12, 6, 6, 6, 10, 21, 21, 21, 21, 21, 21, 21, 10, 10, 10, 4, 4, 4, 3, 6, 6, 12, 12, 12, 6, 21, 21] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 125 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891951 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891951/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891951 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 585) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/585: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2nc(C)c([C@H](C)NC(=O)[C@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)s2)cc1) `ZINC000546891951.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546891951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891951/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000546891951 none COc1ccc(c2nc(C)c([C@H](C)NC(=O)[C@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)s2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 20, 18, 22, 22, 10, 10, 10, 10, 10, 5, 3, 5, 5, 3, 1, 3, 1, 1, 1, 6, 6, 2, 6, 13, 6, 6, 6, 10, 22, 22, 22, 22, 22, 22, 22, 10, 10, 10, 5, 5, 5, 3, 6, 6, 13, 13, 13, 6, 22, 22] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 98 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891951 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546891951 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891951/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891951/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546891951 Building ZINC000546893841 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546893841' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546893841 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546893841 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546893841/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546893841 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 586) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/586 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/586' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(Cc1ccc(Cl)c(Cl)c1)Cc1ccccn1) `ZINC000546893841.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546893841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546893841/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000546893841 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(Cc1ccc(Cl)c(Cl)c1)Cc1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 16, 1, 16, 1, 5, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 2, 2, 4, 10, 27, 27, 27, 27, 27, 27, 27, 4, 8, 12, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 10, 10, 27, 27, 27, 8, 8, 12, 12, 12, 12] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546893841 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546893841/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546893841 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 587) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/587 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/587' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(Cc1ccc(Cl)c(Cl)c1)Cc1ccccn1) `ZINC000546893841.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546893841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546893841/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000546893841 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(Cc1ccc(Cl)c(Cl)c1)Cc1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 16, 1, 16, 1, 5, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 2, 2, 4, 10, 26, 26, 26, 26, 26, 26, 26, 4, 7, 11, 11, 11, 11, 11, 3, 3, 3, 3, 3, 3, 3, 10, 10, 26, 26, 26, 7, 7, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546893841 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546893841 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546893841/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546893841/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546893841 Building ZINC000546893841 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546893841' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546893841 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546893841 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546893841/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546893841 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 586) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/586: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(Cc1ccc(Cl)c(Cl)c1)Cc1ccccn1) `ZINC000546893841.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546893841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546893841/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000546893841 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(Cc1ccc(Cl)c(Cl)c1)Cc1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 16, 1, 16, 1, 5, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 2, 2, 4, 10, 27, 27, 27, 27, 27, 27, 27, 4, 8, 12, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 10, 10, 27, 27, 27, 8, 8, 12, 12, 12, 12] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546893841 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546893841/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546893841 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 587) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/587: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(Cc1ccc(Cl)c(Cl)c1)Cc1ccccn1) `ZINC000546893841.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546893841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546893841/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000546893841 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(Cc1ccc(Cl)c(Cl)c1)Cc1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 16, 1, 16, 1, 5, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 2, 2, 4, 10, 26, 26, 26, 26, 26, 26, 26, 4, 7, 11, 11, 11, 11, 11, 3, 3, 3, 3, 3, 3, 3, 10, 10, 26, 26, 26, 7, 7, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546893841 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546893841 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546893841/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546893841/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546893841 Building ZINC000546895015 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895015' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895015 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546895015 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895015/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895015 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 588) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/588 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/588' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cccc(COCC(F)(F)C(F)F)c2)cc1Cl) `ZINC000546895015.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546895015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895015/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000546895015 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cccc(COCC(F)(F)C(F)F)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 12, 5, 5, 15, 15, 5, 15, 15, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 4, 4, 8, 12, 18, 31, 31, 31, 31, 31, 4, 4, 4, 4, 8, 8, 8, 4, 4, 2, 4, 4, 4, 8, 8, 18, 18, 31, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895015 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895015/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895015 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 589) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/589 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/589' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cccc(COCC(F)(F)C(F)F)c2)cc1Cl) `ZINC000546895015.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546895015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895015/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000546895015 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cccc(COCC(F)(F)C(F)F)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 12, 5, 5, 15, 15, 5, 15, 15, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 4, 4, 8, 12, 17, 31, 31, 31, 31, 31, 4, 4, 4, 4, 6, 6, 6, 4, 4, 2, 4, 4, 4, 8, 8, 17, 17, 31, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895015 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546895015 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895015/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895015/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895015 Building ZINC000546895015 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895015' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895015 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546895015 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895015/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895015 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 588) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/588: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cccc(COCC(F)(F)C(F)F)c2)cc1Cl) `ZINC000546895015.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546895015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895015/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000546895015 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cccc(COCC(F)(F)C(F)F)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 12, 5, 5, 15, 15, 5, 15, 15, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 4, 4, 8, 12, 18, 31, 31, 31, 31, 31, 4, 4, 4, 4, 8, 8, 8, 4, 4, 2, 4, 4, 4, 8, 8, 18, 18, 31, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895015 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895015/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895015 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 589) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/589: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cccc(COCC(F)(F)C(F)F)c2)cc1Cl) `ZINC000546895015.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546895015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895015/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000546895015 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cccc(COCC(F)(F)C(F)F)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 12, 5, 5, 15, 15, 5, 15, 15, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 4, 4, 8, 12, 17, 31, 31, 31, 31, 31, 4, 4, 4, 4, 6, 6, 6, 4, 4, 2, 4, 4, 4, 8, 8, 17, 17, 31, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895015 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546895015 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895015/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895015/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895015 Building ZINC000546895893 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895893' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895893 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546895893 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895893/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895893 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 590) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/590 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/590' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cccc(C[S@@](=O)Cc3ccccc3)c2)cc1Cl) `ZINC000546895893.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546895893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895893/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000546895893 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cccc(C[S@@](=O)Cc3ccccc3)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 10, 13, 13, 25, 27, 27, 25, 27, 27, 7, 6, 6, 6, 12, 12, 12, 6, 6, 2, 7, 7, 7, 10, 10, 25, 25, 27, 27, 25, 27, 27, 7, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895893 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895893/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895893 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 591) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/591 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/591' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cccc(C[S@@](=O)Cc3ccccc3)c2)cc1Cl) `ZINC000546895893.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546895893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895893/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000546895893 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cccc(C[S@@](=O)Cc3ccccc3)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 2, 5, 5, 1, 1, 1, 1, 2, 2, 2, 7, 7, 2, 7, 7, 13, 18, 18, 28, 28, 28, 28, 28, 28, 7, 5, 5, 5, 10, 10, 10, 5, 5, 2, 7, 7, 6, 13, 13, 28, 28, 28, 28, 28, 28, 28, 7, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895893 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546895893 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895893/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895893/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895893 Building ZINC000546895893 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895893' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895893 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546895893 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895893/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895893 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 590) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/590: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cccc(C[S@@](=O)Cc3ccccc3)c2)cc1Cl) `ZINC000546895893.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546895893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895893/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000546895893 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cccc(C[S@@](=O)Cc3ccccc3)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 10, 13, 13, 25, 27, 27, 25, 27, 27, 7, 6, 6, 6, 12, 12, 12, 6, 6, 2, 7, 7, 7, 10, 10, 25, 25, 27, 27, 25, 27, 27, 7, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895893 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895893/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895893 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 591) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/591: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cccc(C[S@@](=O)Cc3ccccc3)c2)cc1Cl) `ZINC000546895893.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546895893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895893/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000546895893 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cccc(C[S@@](=O)Cc3ccccc3)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 2, 5, 5, 1, 1, 1, 1, 2, 2, 2, 7, 7, 2, 7, 7, 13, 18, 18, 28, 28, 28, 28, 28, 28, 7, 5, 5, 5, 10, 10, 10, 5, 5, 2, 7, 7, 6, 13, 13, 28, 28, 28, 28, 28, 28, 28, 7, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895893 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546895893 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895893/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895893/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895893 Building ZINC000546895894 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895894' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895894 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546895894 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895894/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895894 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 592) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/592 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/592' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cccc(C[S@](=O)Cc3ccccc3)c2)cc1Cl) `ZINC000546895894.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546895894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895894/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000546895894 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cccc(C[S@](=O)Cc3ccccc3)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 8, 8, 2, 8, 8, 14, 18, 18, 29, 29, 29, 29, 29, 29, 8, 5, 5, 5, 10, 10, 10, 5, 5, 2, 8, 8, 3, 14, 14, 29, 29, 29, 29, 29, 29, 29, 8, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895894 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895894/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895894 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 593) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/593 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/593' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cccc(C[S@](=O)Cc3ccccc3)c2)cc1Cl) `ZINC000546895894.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546895894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895894/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000546895894 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cccc(C[S@](=O)Cc3ccccc3)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 2, 2, 2, 6, 6, 2, 6, 6, 9, 12, 12, 24, 26, 26, 24, 26, 26, 6, 6, 6, 6, 12, 12, 12, 6, 6, 2, 6, 6, 2, 9, 9, 24, 24, 26, 26, 24, 26, 26, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895894 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546895894 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895894/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895894/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895894 Building ZINC000546895894 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895894' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895894 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546895894 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895894/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895894 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 592) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/592: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cccc(C[S@](=O)Cc3ccccc3)c2)cc1Cl) `ZINC000546895894.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546895894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895894/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000546895894 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cccc(C[S@](=O)Cc3ccccc3)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 8, 8, 2, 8, 8, 14, 18, 18, 29, 29, 29, 29, 29, 29, 8, 5, 5, 5, 10, 10, 10, 5, 5, 2, 8, 8, 3, 14, 14, 29, 29, 29, 29, 29, 29, 29, 8, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895894 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895894/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895894 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 593) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/593: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cccc(C[S@](=O)Cc3ccccc3)c2)cc1Cl) `ZINC000546895894.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546895894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895894/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000546895894 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cccc(C[S@](=O)Cc3ccccc3)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 2, 2, 2, 6, 6, 2, 6, 6, 9, 12, 12, 24, 26, 26, 24, 26, 26, 6, 6, 6, 6, 12, 12, 12, 6, 6, 2, 6, 6, 2, 9, 9, 24, 24, 26, 26, 24, 26, 26, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895894 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546895894 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895894/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895894/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546895894 Building ZINC000470304400 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470304400' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470304400 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000470304400 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470304400/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470304400 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 594) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/594 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/594' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CC(F)(F)F)c1ccccc1C) `ZINC000470304400.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000470304400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470304400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000470304400 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CC(F)(F)F)c1ccccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 12, 12, 4, 12, 12, 4, 4, 1, 1, 1, 1, 7, 7, 7, 13, 13, 20, 20, 20, 20, 13, 18, 18, 18, 18, 18, 18, 4, 4, 4, 12, 12, 7, 12, 12, 4, 4, 4, 7, 20, 20, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 138 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470304400 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470304400/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470304400 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 595) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/595 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/595' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CC(F)(F)F)c1ccccc1C) `ZINC000470304400.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000470304400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470304400/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000470304400 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CC(F)(F)F)c1ccccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 10, 10, 4, 10, 10, 4, 4, 1, 1, 1, 1, 7, 7, 7, 13, 13, 22, 22, 22, 22, 13, 18, 18, 13, 18, 18, 18, 4, 4, 4, 10, 10, 4, 10, 10, 4, 4, 4, 7, 22, 22, 18, 18, 13, 18, 18, 18, 18] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 146 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470304400 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000470304400 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470304400/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470304400/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470304400 Building ZINC000470304400 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470304400' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470304400 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000470304400 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470304400/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470304400 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 594) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/594: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CC(F)(F)F)c1ccccc1C) `ZINC000470304400.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000470304400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470304400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000470304400 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CC(F)(F)F)c1ccccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 12, 12, 4, 12, 12, 4, 4, 1, 1, 1, 1, 7, 7, 7, 13, 13, 20, 20, 20, 20, 13, 18, 18, 18, 18, 18, 18, 4, 4, 4, 12, 12, 7, 12, 12, 4, 4, 4, 7, 20, 20, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 138 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470304400 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470304400/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470304400 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 595) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/595: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CC(F)(F)F)c1ccccc1C) `ZINC000470304400.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000470304400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470304400/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000470304400 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CC(F)(F)F)c1ccccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 10, 10, 4, 10, 10, 4, 4, 1, 1, 1, 1, 7, 7, 7, 13, 13, 22, 22, 22, 22, 13, 18, 18, 13, 18, 18, 18, 4, 4, 4, 10, 10, 4, 10, 10, 4, 4, 4, 7, 22, 22, 18, 18, 13, 18, 18, 18, 18] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 146 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470304400 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000470304400 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470304400/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470304400/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470304400 Building ZINC000470304402 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470304402' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470304402 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000470304402 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470304402/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470304402 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 596) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/596 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/596' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](CC(F)(F)F)c1ccccc1C) `ZINC000470304402.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000470304402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470304402/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000470304402 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](CC(F)(F)F)c1ccccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 10, 10, 4, 10, 10, 4, 4, 1, 1, 1, 1, 7, 7, 7, 13, 13, 22, 22, 22, 22, 13, 18, 18, 18, 18, 18, 18, 4, 4, 4, 10, 10, 7, 10, 10, 4, 4, 4, 7, 22, 22, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 137 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470304402 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470304402/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470304402 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 597) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/597 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/597' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](CC(F)(F)F)c1ccccc1C) `ZINC000470304402.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000470304402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470304402/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000470304402 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](CC(F)(F)F)c1ccccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 11, 11, 4, 11, 11, 4, 4, 1, 1, 1, 1, 8, 8, 8, 14, 14, 21, 21, 21, 21, 14, 19, 19, 14, 19, 19, 19, 4, 4, 4, 11, 11, 4, 11, 11, 4, 4, 4, 8, 21, 21, 19, 19, 14, 19, 19, 19, 19] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 147 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470304402 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000470304402 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470304402/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470304402/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470304402 Building ZINC000470304402 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470304402' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470304402 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000470304402 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470304402/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470304402 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 596) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/596: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](CC(F)(F)F)c1ccccc1C) `ZINC000470304402.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000470304402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470304402/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000470304402 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](CC(F)(F)F)c1ccccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 10, 10, 4, 10, 10, 4, 4, 1, 1, 1, 1, 7, 7, 7, 13, 13, 22, 22, 22, 22, 13, 18, 18, 18, 18, 18, 18, 4, 4, 4, 10, 10, 7, 10, 10, 4, 4, 4, 7, 22, 22, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 137 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470304402 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470304402/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470304402 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 597) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/597: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](CC(F)(F)F)c1ccccc1C) `ZINC000470304402.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000470304402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470304402/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000470304402 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](CC(F)(F)F)c1ccccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 11, 11, 4, 11, 11, 4, 4, 1, 1, 1, 1, 8, 8, 8, 14, 14, 21, 21, 21, 21, 14, 19, 19, 14, 19, 19, 19, 4, 4, 4, 11, 11, 4, 11, 11, 4, 4, 4, 8, 21, 21, 19, 19, 14, 19, 19, 19, 19] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 147 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470304402 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000470304402 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470304402/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470304402/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470304402 Building ZINC000546906653 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546906653' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546906653 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546906653 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546906653/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546906653 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 598) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/598 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/598' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2nc3ccc(OCC(F)(F)F)cc3s2)cc1Cl) `ZINC000546906653.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546906653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546906653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000546906653 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2nc3ccc(OCC(F)(F)F)cc3s2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 1, 14, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 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: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 21, 23, 23, 23, 23, 4, 4, 4, 4, 4, 4, 8, 8, 8, 4, 4, 2, 4, 4, 23, 23, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546906653 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546906653/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546906653 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 599) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/599 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/599' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2nc3ccc(OCC(F)(F)F)cc3s2)cc1Cl) `ZINC000546906653.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546906653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546906653/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000546906653 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2nc3ccc(OCC(F)(F)F)cc3s2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 1, 14, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 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: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 21, 23, 23, 23, 23, 4, 4, 4, 4, 4, 4, 8, 8, 8, 4, 4, 2, 4, 4, 23, 23, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546906653 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546906653 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546906653/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546906653/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546906653 Building ZINC000546906653 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546906653' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546906653 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546906653 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546906653/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546906653 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 598) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/598: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2nc3ccc(OCC(F)(F)F)cc3s2)cc1Cl) `ZINC000546906653.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546906653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546906653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000546906653 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2nc3ccc(OCC(F)(F)F)cc3s2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 1, 14, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 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: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 21, 23, 23, 23, 23, 4, 4, 4, 4, 4, 4, 8, 8, 8, 4, 4, 2, 4, 4, 23, 23, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546906653 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546906653/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546906653 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 599) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/599: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2nc3ccc(OCC(F)(F)F)cc3s2)cc1Cl) `ZINC000546906653.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546906653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546906653/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000546906653 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2nc3ccc(OCC(F)(F)F)cc3s2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 1, 14, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 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: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 21, 23, 23, 23, 23, 4, 4, 4, 4, 4, 4, 8, 8, 8, 4, 4, 2, 4, 4, 23, 23, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546906653 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546906653 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546906653/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546906653/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546906653 Building ZINC000546922524 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546922524' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546922524 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546922524 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546922524/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546922524 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 600) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/600 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/600' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCc3sc(c4csc(C)n4)cc3C2)cc1Cl) `ZINC000546922524.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546922524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546922524/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000546922524 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCc3sc(c4csc(C)n4)cc3C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 14, 1, 1, 1, 14, 1, 5, 8, 1, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 2, 7, 8, 8, 8, 8, 8, 8, 26, 26, 26, 26, 26, 8, 8, 8, 2, 2, 2, 4, 4, 4, 2, 2, 8, 8, 8, 8, 26, 26, 26, 26, 8, 8, 8, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546922524 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546922524/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546922524 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 601) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/601 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/601' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCc3sc(c4csc(C)n4)cc3C2)cc1Cl) `ZINC000546922524.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546922524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546922524/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000546922524 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCc3sc(c4csc(C)n4)cc3C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 14, 1, 1, 1, 14, 1, 5, 8, 1, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 3, 7, 8, 8, 8, 8, 8, 8, 26, 26, 26, 26, 26, 8, 8, 8, 2, 2, 2, 4, 4, 4, 2, 2, 8, 8, 8, 8, 26, 26, 26, 26, 8, 8, 8, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546922524 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546922524 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546922524/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546922524/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546922524 Building ZINC000546922524 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546922524' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546922524 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000546922524 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546922524/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546922524 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 600) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/600: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCc3sc(c4csc(C)n4)cc3C2)cc1Cl) `ZINC000546922524.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000546922524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546922524/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000546922524 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCc3sc(c4csc(C)n4)cc3C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 14, 1, 1, 1, 14, 1, 5, 8, 1, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 2, 7, 8, 8, 8, 8, 8, 8, 26, 26, 26, 26, 26, 8, 8, 8, 2, 2, 2, 4, 4, 4, 2, 2, 8, 8, 8, 8, 26, 26, 26, 26, 8, 8, 8, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546922524 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546922524/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546922524 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 601) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/601: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCc3sc(c4csc(C)n4)cc3C2)cc1Cl) `ZINC000546922524.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000546922524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546922524/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000546922524 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCc3sc(c4csc(C)n4)cc3C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 14, 1, 1, 1, 14, 1, 5, 8, 1, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 3, 7, 8, 8, 8, 8, 8, 8, 26, 26, 26, 26, 26, 8, 8, 8, 2, 2, 2, 4, 4, 4, 2, 2, 8, 8, 8, 8, 26, 26, 26, 26, 8, 8, 8, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546922524 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000546922524 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546922524/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546922524/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000546922524 Building ZINC000470664453 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470664453' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470664453 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000470664453 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470664453/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470664453 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 602) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/602 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/602' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)[C@H](C)c1cccc(c2ccc(OC(C)C)cc2)c1) `ZINC000470664453.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000470664453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470664453/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000470664453 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)[C@H](C)c1cccc(c2ccc(OC(C)C)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 4, 4, 8, 8, 8, 16, 16, 16, 16, 16, 27, 27, 27, 27, 50, 50, 50, 27, 27, 16, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 8, 8, 8, 16, 16, 16, 27, 27, 50, 50, 50, 50, 50, 50, 50, 27, 27, 16] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 110 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470664453 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470664453/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470664453 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 603) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/603 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/603' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)[C@H](C)c1cccc(c2ccc(OC(C)C)cc2)c1) `ZINC000470664453.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000470664453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470664453/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000470664453 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)[C@H](C)c1cccc(c2ccc(OC(C)C)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 4, 4, 5, 5, 5, 16, 16, 16, 16, 16, 26, 26, 16, 26, 45, 45, 45, 26, 26, 16, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 5, 5, 5, 16, 16, 16, 26, 26, 45, 45, 45, 45, 45, 45, 45, 26, 26, 16] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 145 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470664453 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000470664453 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470664453/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470664453/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470664453 Building ZINC000470664453 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470664453' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470664453 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000470664453 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470664453/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470664453 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 602) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/602: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)[C@H](C)c1cccc(c2ccc(OC(C)C)cc2)c1) `ZINC000470664453.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000470664453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470664453/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000470664453 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)[C@H](C)c1cccc(c2ccc(OC(C)C)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 4, 4, 8, 8, 8, 16, 16, 16, 16, 16, 27, 27, 27, 27, 50, 50, 50, 27, 27, 16, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 8, 8, 8, 16, 16, 16, 27, 27, 50, 50, 50, 50, 50, 50, 50, 27, 27, 16] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 110 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470664453 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470664453/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470664453 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 603) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/603: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)[C@H](C)c1cccc(c2ccc(OC(C)C)cc2)c1) `ZINC000470664453.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000470664453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470664453/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000470664453 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)[C@H](C)c1cccc(c2ccc(OC(C)C)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 4, 4, 5, 5, 5, 16, 16, 16, 16, 16, 26, 26, 16, 26, 45, 45, 45, 26, 26, 16, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 5, 5, 5, 16, 16, 16, 26, 26, 45, 45, 45, 45, 45, 45, 45, 26, 26, 16] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 145 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470664453 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000470664453 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470664453/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470664453/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470664453 Building ZINC000470664454 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470664454' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470664454 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000470664454 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470664454/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470664454 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 604) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/604 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/604' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)[C@@H](C)c1cccc(c2ccc(OC(C)C)cc2)c1) `ZINC000470664454.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000470664454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470664454/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000470664454 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)[C@@H](C)c1cccc(c2ccc(OC(C)C)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 5, 5, 6, 6, 6, 15, 15, 15, 15, 15, 23, 23, 23, 23, 42, 43, 43, 23, 23, 15, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 6, 6, 6, 15, 15, 15, 23, 23, 43, 43, 43, 43, 43, 43, 43, 23, 23, 15] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 95 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470664454 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470664454/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470664454 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 605) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/605 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/605' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)[C@@H](C)c1cccc(c2ccc(OC(C)C)cc2)c1) `ZINC000470664454.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000470664454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470664454/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000470664454 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)[C@@H](C)c1cccc(c2ccc(OC(C)C)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 4, 4, 8, 8, 8, 17, 17, 17, 17, 17, 28, 28, 17, 17, 50, 50, 50, 28, 28, 17, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 8, 8, 8, 17, 17, 17, 28, 28, 50, 50, 50, 50, 50, 50, 50, 28, 28, 17] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 147 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470664454 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000470664454 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470664454/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470664454/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470664454 Building ZINC000470664454 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470664454' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470664454 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000470664454 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470664454/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470664454 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 604) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/604: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)[C@@H](C)c1cccc(c2ccc(OC(C)C)cc2)c1) `ZINC000470664454.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000470664454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470664454/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000470664454 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)[C@@H](C)c1cccc(c2ccc(OC(C)C)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 5, 5, 6, 6, 6, 15, 15, 15, 15, 15, 23, 23, 23, 23, 42, 43, 43, 23, 23, 15, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 6, 6, 6, 15, 15, 15, 23, 23, 43, 43, 43, 43, 43, 43, 43, 23, 23, 15] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 95 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470664454 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470664454/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470664454 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 605) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/605: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)[C@@H](C)c1cccc(c2ccc(OC(C)C)cc2)c1) `ZINC000470664454.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000470664454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470664454/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000470664454 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)[C@@H](C)c1cccc(c2ccc(OC(C)C)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 4, 4, 8, 8, 8, 17, 17, 17, 17, 17, 28, 28, 17, 17, 50, 50, 50, 28, 28, 17, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 8, 8, 8, 17, 17, 17, 28, 28, 50, 50, 50, 50, 50, 50, 50, 28, 28, 17] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 147 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470664454 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000470664454 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470664454/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470664454/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470664454 Building ZINC000547408522 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000547408522' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000547408522 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000547408522 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000547408522/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000547408522 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 606) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/606 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/606' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1c(c2ccccc2)nc2ccccn21) `ZINC000547408522.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000547408522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000547408522/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000547408522 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1c(c2ccccc2)nc2ccccn21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', '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', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 10, 10, 4, 10, 10, 4, 4, 1, 1, 1, 1, 6, 6, 13, 22, 22, 34, 34, 22, 34, 34, 22, 22, 22, 22, 22, 22, 22, 4, 4, 4, 10, 10, 4, 10, 10, 4, 4, 4, 13, 34, 34, 22, 34, 34, 22, 22, 22, 22] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 130 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000547408522 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000547408522/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000547408522 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 607) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/607 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/607' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1c(c2ccccc2)nc2ccccn21) `ZINC000547408522.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000547408522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000547408522/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000547408522 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1c(c2ccccc2)nc2ccccn21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', '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', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 5, 9, 9, 3, 3, 1, 1, 1, 1, 6, 6, 14, 22, 22, 35, 35, 32, 35, 35, 22, 22, 22, 22, 22, 22, 22, 3, 3, 3, 9, 9, 6, 9, 9, 3, 3, 3, 14, 35, 35, 32, 35, 35, 22, 22, 22, 22] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 110 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000547408522 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000547408522 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000547408522/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000547408522/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000547408522 Building ZINC000547408522 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000547408522' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000547408522 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000547408522 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000547408522/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000547408522 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 606) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/606: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1c(c2ccccc2)nc2ccccn21) `ZINC000547408522.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000547408522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000547408522/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000547408522 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1c(c2ccccc2)nc2ccccn21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', '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', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 10, 10, 4, 10, 10, 4, 4, 1, 1, 1, 1, 6, 6, 13, 22, 22, 34, 34, 22, 34, 34, 22, 22, 22, 22, 22, 22, 22, 4, 4, 4, 10, 10, 4, 10, 10, 4, 4, 4, 13, 34, 34, 22, 34, 34, 22, 22, 22, 22] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 130 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000547408522 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000547408522/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000547408522 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 607) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/607: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1c(c2ccccc2)nc2ccccn21) `ZINC000547408522.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000547408522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000547408522/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000547408522 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1c(c2ccccc2)nc2ccccn21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', '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', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 5, 9, 9, 3, 3, 1, 1, 1, 1, 6, 6, 14, 22, 22, 35, 35, 32, 35, 35, 22, 22, 22, 22, 22, 22, 22, 3, 3, 3, 9, 9, 6, 9, 9, 3, 3, 3, 14, 35, 35, 32, 35, 35, 22, 22, 22, 22] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 110 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000547408522 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000547408522 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000547408522/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000547408522/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000547408522 Building ZINC000470908470 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470908470' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470908470 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000470908470 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470908470/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470908470 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 608) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/608 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/608' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ccc(O)c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1) `ZINC000470908470.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000470908470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470908470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000470908470 none CCc1ccc(O)c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 12, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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, 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: [11, 6, 6, 3, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 6, 11, 11, 11, 11, 11, 6, 6, 12, 2, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2, 6] 100 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470908470 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470908470/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470908470 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 609) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/609 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/609' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ccc(O)c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1) `ZINC000470908470.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000470908470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470908470/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000470908470 none CCc1ccc(O)c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 12, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [9, 6, 6, 6, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 18, 18, 3, 18, 18, 18, 18, 18, 18, 3, 3, 6, 9, 9, 9, 9, 9, 6, 6, 12, 2, 3, 3, 3, 18, 18, 5, 18, 3, 3, 3, 6] 100 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 87 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470908470 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000470908470 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470908470/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470908470/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470908470 Building ZINC000470908470 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470908470' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470908470 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000470908470 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470908470/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470908470 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 608) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/608: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ccc(O)c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1) `ZINC000470908470.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000470908470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470908470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000470908470 none CCc1ccc(O)c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 12, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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, 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: [11, 6, 6, 3, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 6, 11, 11, 11, 11, 11, 6, 6, 12, 2, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2, 6] 100 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470908470 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470908470/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470908470 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 609) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/609: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ccc(O)c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1) `ZINC000470908470.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000470908470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470908470/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000470908470 none CCc1ccc(O)c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 12, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [9, 6, 6, 6, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 18, 18, 3, 18, 18, 18, 18, 18, 18, 3, 3, 6, 9, 9, 9, 9, 9, 6, 6, 12, 2, 3, 3, 3, 18, 18, 5, 18, 3, 3, 3, 6] 100 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 87 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470908470 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000470908470 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470908470/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470908470/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000470908470 Building ZINC000557437878 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437878' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437878 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000557437878 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437878/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437878 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 610) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/610 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/610' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](c3cccc(C(F)(F)F)c3)OC[C@@H]2C)cc1Cl) `ZINC000557437878.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000557437878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437878/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000557437878 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](c3cccc(C(F)(F)F)c3)OC[C@@H]2C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 2, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 26, 26, 3, 26, 26, 26, 26, 26, 26, 3, 3, 3, 3, 3, 2, 2, 2, 6, 6, 6, 2, 2, 3, 3, 26, 26, 3, 26, 3, 3, 3, 3, 3, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 69 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437878 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437878/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437878 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 611) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/611 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/611' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](c3cccc(C(F)(F)F)c3)OC[C@@H]2C)cc1Cl) `ZINC000557437878.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000557437878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437878/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000557437878 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](c3cccc(C(F)(F)F)c3)OC[C@@H]2C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 17, 17, 2, 17, 17, 17, 17, 17, 17, 2, 2, 2, 2, 2, 6, 6, 6, 13, 13, 13, 6, 6, 2, 2, 17, 17, 2, 17, 2, 2, 2, 2, 2, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437878 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000557437878 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437878/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437878/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437878 Building ZINC000557437878 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437878' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437878 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000557437878 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437878/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437878 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 610) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/610: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](c3cccc(C(F)(F)F)c3)OC[C@@H]2C)cc1Cl) `ZINC000557437878.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000557437878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437878/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000557437878 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](c3cccc(C(F)(F)F)c3)OC[C@@H]2C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 2, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 26, 26, 3, 26, 26, 26, 26, 26, 26, 3, 3, 3, 3, 3, 2, 2, 2, 6, 6, 6, 2, 2, 3, 3, 26, 26, 3, 26, 3, 3, 3, 3, 3, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 69 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437878 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437878/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437878 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 611) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/611: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](c3cccc(C(F)(F)F)c3)OC[C@@H]2C)cc1Cl) `ZINC000557437878.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000557437878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437878/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000557437878 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](c3cccc(C(F)(F)F)c3)OC[C@@H]2C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 17, 17, 2, 17, 17, 17, 17, 17, 17, 2, 2, 2, 2, 2, 6, 6, 6, 13, 13, 13, 6, 6, 2, 2, 17, 17, 2, 17, 2, 2, 2, 2, 2, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437878 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000557437878 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437878/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437878/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437878 Building ZINC000557437879 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437879' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437879 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000557437879 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437879/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437879 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 612) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/612 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/612' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](c3cccc(C(F)(F)F)c3)OC[C@H]2C)cc1Cl) `ZINC000557437879.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000557437879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437879/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000557437879 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](c3cccc(C(F)(F)F)c3)OC[C@H]2C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 2, 2, 2, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 26, 26, 4, 26, 26, 26, 26, 26, 26, 3, 3, 3, 3, 3, 2, 2, 2, 5, 5, 5, 2, 2, 3, 3, 26, 26, 4, 26, 3, 3, 3, 3, 3, 2] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437879 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437879/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437879 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 613) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/613 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/613' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](c3cccc(C(F)(F)F)c3)OC[C@H]2C)cc1Cl) `ZINC000557437879.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000557437879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437879/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000557437879 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](c3cccc(C(F)(F)F)c3)OC[C@H]2C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 2, 3, 3, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 26, 26, 5, 26, 26, 26, 26, 26, 26, 5, 5, 5, 5, 5, 3, 3, 3, 7, 7, 7, 3, 3, 5, 5, 26, 26, 5, 26, 5, 5, 5, 5, 5, 3] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437879 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000557437879 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437879/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437879/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437879 Building ZINC000557437879 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437879' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437879 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000557437879 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437879/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437879 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 612) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/612: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](c3cccc(C(F)(F)F)c3)OC[C@H]2C)cc1Cl) `ZINC000557437879.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000557437879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437879/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000557437879 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@H](c3cccc(C(F)(F)F)c3)OC[C@H]2C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 2, 2, 2, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 26, 26, 4, 26, 26, 26, 26, 26, 26, 3, 3, 3, 3, 3, 2, 2, 2, 5, 5, 5, 2, 2, 3, 3, 26, 26, 4, 26, 3, 3, 3, 3, 3, 2] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437879 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437879/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437879 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 613) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/613: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](c3cccc(C(F)(F)F)c3)OC[C@H]2C)cc1Cl) `ZINC000557437879.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000557437879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437879/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000557437879 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](c3cccc(C(F)(F)F)c3)OC[C@H]2C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 2, 3, 3, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 26, 26, 5, 26, 26, 26, 26, 26, 26, 5, 5, 5, 5, 5, 3, 3, 3, 7, 7, 7, 3, 3, 5, 5, 26, 26, 5, 26, 5, 5, 5, 5, 5, 3] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437879 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000557437879 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437879/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437879/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437879 Building ZINC000557437880 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437880' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437880 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000557437880 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437880/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437880 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 614) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/614 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/614' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](c3cccc(C(F)(F)F)c3)OC[C@@H]2C)cc1Cl) `ZINC000557437880.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000557437880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000557437880 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](c3cccc(C(F)(F)F)c3)OC[C@@H]2C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 2, 1, 1, 1, 2, 6, 6, 6, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 6, 6, 6, 6, 6, 2, 2, 2, 6, 6, 6, 2, 2, 6, 6, 27, 27, 27, 27, 6, 6, 6, 6, 6, 2] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437880 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437880/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437880 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 615) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/615 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/615' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](c3cccc(C(F)(F)F)c3)OC[C@@H]2C)cc1Cl) `ZINC000557437880.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000557437880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437880/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000557437880 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](c3cccc(C(F)(F)F)c3)OC[C@@H]2C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 2, 2, 2, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 26, 26, 4, 26, 26, 26, 26, 26, 26, 4, 4, 4, 4, 4, 2, 2, 2, 5, 5, 5, 2, 2, 4, 4, 26, 26, 4, 26, 4, 4, 4, 4, 4, 2] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437880 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000557437880 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437880/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437880/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437880 Building ZINC000557437880 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437880' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437880 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000557437880 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437880/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437880 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 614) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/614: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](c3cccc(C(F)(F)F)c3)OC[C@@H]2C)cc1Cl) `ZINC000557437880.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000557437880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000557437880 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](c3cccc(C(F)(F)F)c3)OC[C@@H]2C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 2, 1, 1, 1, 2, 6, 6, 6, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 6, 6, 6, 6, 6, 2, 2, 2, 6, 6, 6, 2, 2, 6, 6, 27, 27, 27, 27, 6, 6, 6, 6, 6, 2] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437880 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437880/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437880 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 615) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/615: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](c3cccc(C(F)(F)F)c3)OC[C@@H]2C)cc1Cl) `ZINC000557437880.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000557437880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437880/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000557437880 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](c3cccc(C(F)(F)F)c3)OC[C@@H]2C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 2, 2, 2, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 26, 26, 4, 26, 26, 26, 26, 26, 26, 4, 4, 4, 4, 4, 2, 2, 2, 5, 5, 5, 2, 2, 4, 4, 26, 26, 4, 26, 4, 4, 4, 4, 4, 2] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437880 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000557437880 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437880/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437880/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437880 Building ZINC000557437881 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437881' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437881 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000557437881 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437881/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437881 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 616) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/616 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/616' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](c3cccc(C(F)(F)F)c3)OC[C@H]2C)cc1Cl) `ZINC000557437881.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000557437881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000557437881 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](c3cccc(C(F)(F)F)c3)OC[C@H]2C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 16, 16, 2, 16, 16, 16, 16, 16, 16, 2, 2, 2, 2, 2, 6, 6, 6, 13, 13, 13, 6, 6, 2, 2, 16, 16, 2, 16, 2, 2, 2, 2, 2, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437881 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437881/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437881 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 617) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/617 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/617' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](c3cccc(C(F)(F)F)c3)OC[C@H]2C)cc1Cl) `ZINC000557437881.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000557437881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437881/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000557437881 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](c3cccc(C(F)(F)F)c3)OC[C@H]2C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 2, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 26, 26, 3, 26, 26, 26, 26, 26, 26, 3, 3, 3, 3, 3, 2, 2, 2, 6, 6, 6, 2, 2, 3, 3, 26, 26, 3, 26, 3, 3, 3, 3, 3, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 69 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437881 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000557437881 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437881/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437881/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437881 Building ZINC000557437881 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437881' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437881 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000557437881 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437881/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437881 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 616) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/616: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](c3cccc(C(F)(F)F)c3)OC[C@H]2C)cc1Cl) `ZINC000557437881.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000557437881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000557437881 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](c3cccc(C(F)(F)F)c3)OC[C@H]2C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 16, 16, 2, 16, 16, 16, 16, 16, 16, 2, 2, 2, 2, 2, 6, 6, 6, 13, 13, 13, 6, 6, 2, 2, 16, 16, 2, 16, 2, 2, 2, 2, 2, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437881 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437881/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437881 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 617) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/617: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](c3cccc(C(F)(F)F)c3)OC[C@H]2C)cc1Cl) `ZINC000557437881.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000557437881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437881/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000557437881 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](c3cccc(C(F)(F)F)c3)OC[C@H]2C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 2, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 26, 26, 3, 26, 26, 26, 26, 26, 26, 3, 3, 3, 3, 3, 2, 2, 2, 6, 6, 6, 2, 2, 3, 3, 26, 26, 3, 26, 3, 3, 3, 3, 3, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 69 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437881 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000557437881 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437881/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437881/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000557437881 Building ZINC000559671368 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000559671368' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000559671368 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000559671368 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000559671368/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000559671368 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 618) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/618 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/618' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC(C)(C)c1cccc(C(F)(F)F)c1) `ZINC000559671368.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000559671368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000559671368/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000559671368 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC(C)(C)c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 44, 44, 13, 44, 44, 44, 44, 44, 44, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 2, 4, 8, 8, 8, 8, 8, 8, 44, 44, 19, 44] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 141 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000559671368 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000559671368/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000559671368 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 619) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/619 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/619' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC(C)(C)c1cccc(C(F)(F)F)c1) `ZINC000559671368.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000559671368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000559671368/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000559671368 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC(C)(C)c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 41, 41, 12, 41, 41, 41, 41, 41, 41, 2, 2, 2, 5, 5, 3, 5, 5, 2, 2, 2, 4, 8, 8, 8, 8, 8, 8, 41, 41, 18, 41] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 134 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000559671368 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000559671368 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000559671368/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000559671368/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000559671368 Building ZINC000559671368 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000559671368' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000559671368 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000559671368 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000559671368/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000559671368 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 618) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/618: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC(C)(C)c1cccc(C(F)(F)F)c1) `ZINC000559671368.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000559671368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000559671368/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000559671368 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC(C)(C)c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 44, 44, 13, 44, 44, 44, 44, 44, 44, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 2, 4, 8, 8, 8, 8, 8, 8, 44, 44, 19, 44] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 141 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000559671368 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000559671368/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000559671368 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 619) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/619: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC(C)(C)c1cccc(C(F)(F)F)c1) `ZINC000559671368.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000559671368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000559671368/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000559671368 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC(C)(C)c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 41, 41, 12, 41, 41, 41, 41, 41, 41, 2, 2, 2, 5, 5, 3, 5, 5, 2, 2, 2, 4, 8, 8, 8, 8, 8, 8, 41, 41, 18, 41] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 134 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000559671368 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000559671368 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000559671368/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000559671368/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000559671368 Building ZINC000777782547 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000777782547' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000777782547 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000777782547 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000777782547/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000777782547 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 620) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/620 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/620' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC=C(c2ccccc2)C1) `ZINC000777782547.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000777782547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000777782547/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000777782547 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC=C(c2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 22, 22, 3, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 9, 9, 4, 9, 9, 4, 3, 3, 3, 22, 22, 3, 22, 3, 3, 3, 4, 4, 4, 9, 9, 4, 9, 9, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 71 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000777782547 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000777782547/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000777782547 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 621) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/621 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/621' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC=C(c2ccccc2)C1) `ZINC000777782547.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000777782547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000777782547/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000777782547 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC=C(c2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 22, 22, 3, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 9, 9, 4, 9, 9, 4, 3, 3, 3, 22, 22, 3, 22, 3, 3, 3, 4, 4, 4, 9, 9, 4, 9, 9, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 71 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000777782547 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000777782547 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000777782547/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000777782547/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000777782547 Building ZINC000777782547 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000777782547' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000777782547 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000777782547 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000777782547/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000777782547 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 620) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/620: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC=C(c2ccccc2)C1) `ZINC000777782547.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000777782547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000777782547/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000777782547 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC=C(c2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 22, 22, 3, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 9, 9, 4, 9, 9, 4, 3, 3, 3, 22, 22, 3, 22, 3, 3, 3, 4, 4, 4, 9, 9, 4, 9, 9, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 71 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000777782547 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000777782547/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000777782547 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 621) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/621: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC=C(c2ccccc2)C1) `ZINC000777782547.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000777782547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000777782547/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000777782547 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC=C(c2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 22, 22, 3, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 9, 9, 4, 9, 9, 4, 3, 3, 3, 22, 22, 3, 22, 3, 3, 3, 4, 4, 4, 9, 9, 4, 9, 9, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 71 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000777782547 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000777782547 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000777782547/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000777782547/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000777782547 Building ZINC000561410882 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000561410882' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000561410882 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000561410882 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000561410882/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000561410882 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 622) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/622 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/622' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](OCc2ccccc2)c2ccc(Cl)cc2)cn1) `ZINC000561410882.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000561410882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000561410882/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000561410882 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](OCc2ccccc2)c2ccc(Cl)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 9, 9, 6, 6, 1, 1, 1, 1, 2, 2, 2, 7, 9, 9, 14, 26, 40, 40, 28, 40, 40, 9, 9, 9, 9, 9, 9, 9, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 2, 7, 7, 26, 26, 40, 40, 40, 40, 40, 9, 9, 9, 9, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000561410882 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000561410882/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000561410882 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 623) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/623 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/623' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC[C@H](OCc2ccccc2)c2ccc(Cl)cc2)cn1) `ZINC000561410882.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000561410882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000561410882/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000561410882 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC[C@H](OCc2ccccc2)c2ccc(Cl)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 11, 11, 6, 6, 1, 1, 1, 1, 3, 3, 3, 7, 10, 10, 14, 27, 39, 39, 30, 39, 39, 10, 10, 10, 10, 10, 10, 10, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 3, 7, 7, 27, 27, 39, 39, 39, 39, 39, 10, 10, 10, 10, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 205 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000561410882 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000561410882 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000561410882/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000561410882/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000561410882 Building ZINC000561410882 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000561410882' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000561410882 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000561410882 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000561410882/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000561410882 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 622) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/622: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](OCc2ccccc2)c2ccc(Cl)cc2)cn1) `ZINC000561410882.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000561410882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000561410882/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000561410882 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](OCc2ccccc2)c2ccc(Cl)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 9, 9, 6, 6, 1, 1, 1, 1, 2, 2, 2, 7, 9, 9, 14, 26, 40, 40, 28, 40, 40, 9, 9, 9, 9, 9, 9, 9, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 2, 7, 7, 26, 26, 40, 40, 40, 40, 40, 9, 9, 9, 9, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000561410882 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000561410882/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000561410882 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 623) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/623: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC[C@H](OCc2ccccc2)c2ccc(Cl)cc2)cn1) `ZINC000561410882.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000561410882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000561410882/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000561410882 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC[C@H](OCc2ccccc2)c2ccc(Cl)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 11, 11, 6, 6, 1, 1, 1, 1, 3, 3, 3, 7, 10, 10, 14, 27, 39, 39, 30, 39, 39, 10, 10, 10, 10, 10, 10, 10, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 3, 7, 7, 27, 27, 39, 39, 39, 39, 39, 10, 10, 10, 10, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 205 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000561410882 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000561410882 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000561410882/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000561410882/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000561410882 Building ZINC000561410884 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000561410884' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000561410884 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000561410884 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000561410884/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000561410884 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 624) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/624 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/624' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H](OCc2ccccc2)c2ccc(Cl)cc2)cn1) `ZINC000561410884.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000561410884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000561410884/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000561410884 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H](OCc2ccccc2)c2ccc(Cl)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 1, 1, 1, 1, 3, 3, 3, 7, 10, 10, 13, 27, 40, 40, 30, 40, 40, 10, 10, 10, 10, 10, 10, 10, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 3, 7, 7, 27, 27, 40, 40, 40, 40, 40, 10, 10, 10, 10, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000561410884 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000561410884/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000561410884 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 625) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/625 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/625' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC[C@@H](OCc2ccccc2)c2ccc(Cl)cc2)cn1) `ZINC000561410884.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000561410884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000561410884/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000561410884 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC[C@@H](OCc2ccccc2)c2ccc(Cl)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 1, 1, 1, 1, 2, 2, 2, 7, 9, 9, 14, 26, 40, 40, 29, 40, 40, 9, 9, 9, 9, 9, 9, 9, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 2, 7, 7, 26, 26, 40, 40, 40, 40, 40, 9, 9, 9, 9, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000561410884 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000561410884 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000561410884/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000561410884/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000561410884 Building ZINC000561410884 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000561410884' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000561410884 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000561410884 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000561410884/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000561410884 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 624) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/624: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H](OCc2ccccc2)c2ccc(Cl)cc2)cn1) `ZINC000561410884.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000561410884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000561410884/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000561410884 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H](OCc2ccccc2)c2ccc(Cl)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 1, 1, 1, 1, 3, 3, 3, 7, 10, 10, 13, 27, 40, 40, 30, 40, 40, 10, 10, 10, 10, 10, 10, 10, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 3, 7, 7, 27, 27, 40, 40, 40, 40, 40, 10, 10, 10, 10, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000561410884 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000561410884/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000561410884 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 625) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/625: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC[C@@H](OCc2ccccc2)c2ccc(Cl)cc2)cn1) `ZINC000561410884.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000561410884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000561410884/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000561410884 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC[C@@H](OCc2ccccc2)c2ccc(Cl)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 1, 1, 1, 1, 2, 2, 2, 7, 9, 9, 14, 26, 40, 40, 29, 40, 40, 9, 9, 9, 9, 9, 9, 9, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 2, 7, 7, 26, 26, 40, 40, 40, 40, 40, 9, 9, 9, 9, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000561410884 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000561410884 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000561410884/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000561410884/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000561410884 Building ZINC000778242411 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000778242411' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000778242411 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000778242411 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000778242411/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000778242411 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 626) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/626 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/626' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(c2ccc(Br)cc2)c(C)c1) `ZINC000778242411.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000778242411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000778242411/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000778242411 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(c2ccc(Br)cc2)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 8, 8, 8, 42, 42, 10, 14, 40, 40, 40, 40, 40, 40, 42, 42, 42, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 42, 42, 40, 40, 40, 40, 42, 42, 42, 42] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 150 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000778242411 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000778242411/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000778242411 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 627) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/627 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/627' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(c2ccc(Br)cc2)c(C)c1) `ZINC000778242411.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000778242411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000778242411/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000778242411 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(c2ccc(Br)cc2)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 8, 8, 8, 42, 42, 42, 42, 46, 46, 44, 46, 46, 46, 42, 42, 42, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 42, 42, 46, 46, 46, 46, 42, 42, 42, 42] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 82 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000778242411 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000778242411 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000778242411/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000778242411/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000778242411 Building ZINC000778242411 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000778242411' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000778242411 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000778242411 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000778242411/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000778242411 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 626) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/626: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(c2ccc(Br)cc2)c(C)c1) `ZINC000778242411.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000778242411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000778242411/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000778242411 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(c2ccc(Br)cc2)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 8, 8, 8, 42, 42, 10, 14, 40, 40, 40, 40, 40, 40, 42, 42, 42, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 42, 42, 40, 40, 40, 40, 42, 42, 42, 42] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 150 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000778242411 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000778242411/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000778242411 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 627) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/627: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(c2ccc(Br)cc2)c(C)c1) `ZINC000778242411.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000778242411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000778242411/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000778242411 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(c2ccc(Br)cc2)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 8, 8, 8, 42, 42, 42, 42, 46, 46, 44, 46, 46, 46, 42, 42, 42, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 42, 42, 46, 46, 46, 46, 42, 42, 42, 42] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 82 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000778242411 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000778242411 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000778242411/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000778242411/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000778242411 Building ZINC000564029621 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000564029621' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000564029621 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000564029621 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000564029621/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000564029621 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 628) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/628 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/628' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C1CCC(F)(F)CC1) `ZINC000564029621.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000564029621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000564029621/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000564029621 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C1CCC(F)(F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 15, 15, 3, 15, 15, 15, 15, 15, 15, 3, 3, 1, 1, 1, 1, 3, 3, 7, 7, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 15, 15, 3, 15, 3, 3, 3, 7, 7, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 65 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000564029621 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000564029621/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000564029621 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 629) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/629 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/629' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C1CCC(F)(F)CC1) `ZINC000564029621.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000564029621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000564029621/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000564029621 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C1CCC(F)(F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 3, 3, 7, 7, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 7, 7, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 59 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000564029621 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000564029621 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000564029621/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000564029621/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000564029621 Building ZINC000564029621 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000564029621' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000564029621 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000564029621 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000564029621/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000564029621 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 628) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/628: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C1CCC(F)(F)CC1) `ZINC000564029621.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000564029621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000564029621/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000564029621 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C1CCC(F)(F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 15, 15, 3, 15, 15, 15, 15, 15, 15, 3, 3, 1, 1, 1, 1, 3, 3, 7, 7, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 15, 15, 3, 15, 3, 3, 3, 7, 7, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 65 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000564029621 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000564029621/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000564029621 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 629) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/629: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C1CCC(F)(F)CC1) `ZINC000564029621.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000564029621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000564029621/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000564029621 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C1CCC(F)(F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 3, 3, 7, 7, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 7, 7, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 59 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000564029621 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000564029621 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000564029621/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000564029621/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000564029621 Building ZINC000565123548 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000565123548' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000565123548 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000565123548 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000565123548/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000565123548 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 630) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/630 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/630' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nnc(c2cccc(OC(F)(F)F)c2)s1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000565123548.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000565123548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000565123548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000565123548 none O=C(Nc1nnc(c2cccc(OC(F)(F)F)c2)s1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 14, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 4, 4, 15, 15, 15, 15, 15, 50, 50, 50, 50, 15, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 15, 15, 15, 15, 2, 2, 2, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000565123548 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000565123548/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000565123548 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 631) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/631 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/631' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nnc(c2cccc(OC(F)(F)F)c2)s1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000565123548.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000565123548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000565123548/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000565123548 none O=C(Nc1nnc(c2cccc(OC(F)(F)F)c2)s1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 14, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 4, 4, 15, 15, 15, 15, 15, 50, 50, 50, 50, 15, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 15, 15, 15, 15, 2, 2, 2, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000565123548 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000565123548 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000565123548/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000565123548/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000565123548 Building ZINC000565123548 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000565123548' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000565123548 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000565123548 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000565123548/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000565123548 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 630) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/630: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nnc(c2cccc(OC(F)(F)F)c2)s1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000565123548.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000565123548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000565123548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000565123548 none O=C(Nc1nnc(c2cccc(OC(F)(F)F)c2)s1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 14, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 4, 4, 15, 15, 15, 15, 15, 50, 50, 50, 50, 15, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 15, 15, 15, 15, 2, 2, 2, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000565123548 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000565123548/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000565123548 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 631) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/631: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nnc(c2cccc(OC(F)(F)F)c2)s1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000565123548.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000565123548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000565123548/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000565123548 none O=C(Nc1nnc(c2cccc(OC(F)(F)F)c2)s1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 14, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 4, 4, 15, 15, 15, 15, 15, 50, 50, 50, 50, 15, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 15, 15, 15, 15, 2, 2, 2, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000565123548 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000565123548 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000565123548/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000565123548/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000565123548 Building ZINC000565854804 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000565854804' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000565854804 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000565854804 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000565854804/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000565854804 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 632) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/632 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/632' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)ccc1F) `ZINC000565854804.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000565854804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000565854804/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000565854804 none CC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 7, 13, 7, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 7, 7, 7, 7, 13, 13, 13, 7, 2, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 7, 7] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000565854804 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000565854804/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000565854804 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 633) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/633 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/633' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)ccc1F) `ZINC000565854804.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000565854804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000565854804/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000565854804 none CC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 7, 7, 7, 7, 12, 12, 12, 7, 2, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 7, 7] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000565854804 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000565854804 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000565854804/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000565854804/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000565854804 Building ZINC000565854804 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000565854804' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000565854804 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000565854804 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000565854804/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000565854804 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 632) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/632: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)ccc1F) `ZINC000565854804.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000565854804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000565854804/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000565854804 none CC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 7, 13, 7, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 7, 7, 7, 7, 13, 13, 13, 7, 2, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 7, 7] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000565854804 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000565854804/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000565854804 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 633) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/633: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)ccc1F) `ZINC000565854804.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000565854804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000565854804/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000565854804 none CC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 7, 7, 7, 7, 12, 12, 12, 7, 2, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 7, 7] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000565854804 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000565854804 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000565854804/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000565854804/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000565854804 Building ZINC000568297490 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000568297490 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 634) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/634 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/634' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(CC2CN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)C2)c2cc(C3CC3)ccc21) `ZINC000568297490.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000568297490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000568297490 none CC1(C)CN(CC2CN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)C2)c2cc(C3CC3)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 1, 1, 1, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 4, 4, 4, 1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 47, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 16, 16, 4, 4, 4, 2, 2, 4, 4, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [8, 9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 635) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/635 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/635' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(CC2CN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)C2)c2cc(C3CC3)ccc21) `ZINC000568297490.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000568297490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000568297490 none CC1(C)CN(CC2CN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)C2)c2cc(C3CC3)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 1, 1, 1, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 4, 4, 4, 1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 47, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 16, 16, 4, 4, 4, 2, 2, 4, 4, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [8, 9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 636) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/636 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/636' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(CC2CN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)C2)c2cc(C3CC3)ccc21) `ZINC000568297490.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000568297490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000568297490 none CC1(C)CN(CC2CN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)C2)c2cc(C3CC3)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 1, 1, 1, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 15, 4, 4, 4, 1, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 4, 4, 4, 1, 1, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [43, 8, 9, 42, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 637) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/637 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/637' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(CC2CN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)C2)c2cc(C3CC3)ccc21) `ZINC000568297490.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000568297490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000568297490 none CC1(C)CN(CC2CN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)C2)c2cc(C3CC3)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 1, 1, 1, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 15, 4, 4, 4, 1, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 4, 4, 4, 1, 1, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [43, 8, 9, 42, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000568297490 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490 Building ZINC000568297490 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000568297490 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 634) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/634: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(CC2CN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)C2)c2cc(C3CC3)ccc21) `ZINC000568297490.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000568297490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000568297490 none CC1(C)CN(CC2CN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)C2)c2cc(C3CC3)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 1, 1, 1, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 4, 4, 4, 1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 47, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 16, 16, 4, 4, 4, 2, 2, 4, 4, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [8, 9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 635) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/635: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(CC2CN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)C2)c2cc(C3CC3)ccc21) `ZINC000568297490.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000568297490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000568297490 none CC1(C)CN(CC2CN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)C2)c2cc(C3CC3)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 1, 1, 1, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 4, 4, 4, 1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 47, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 16, 16, 4, 4, 4, 2, 2, 4, 4, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [8, 9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 636) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/636: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(CC2CN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)C2)c2cc(C3CC3)ccc21) `ZINC000568297490.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000568297490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000568297490 none CC1(C)CN(CC2CN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)C2)c2cc(C3CC3)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 1, 1, 1, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 15, 4, 4, 4, 1, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 4, 4, 4, 1, 1, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [43, 8, 9, 42, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 637) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/637: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(CC2CN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)C2)c2cc(C3CC3)ccc21) `ZINC000568297490.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000568297490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000568297490 none CC1(C)CN(CC2CN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)C2)c2cc(C3CC3)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 1, 1, 1, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 15, 4, 4, 4, 1, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 4, 4, 4, 1, 1, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [43, 8, 9, 42, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000568297490 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490 Building ZINC000568297490 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000568297490 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 634) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/634: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(CC2CN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)C2)c2cc(C3CC3)ccc21) `ZINC000568297490.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000568297490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000568297490 none CC1(C)CN(CC2CN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)C2)c2cc(C3CC3)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 1, 1, 1, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 4, 4, 4, 1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 47, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 16, 16, 4, 4, 4, 2, 2, 4, 4, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [8, 9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 635) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/635: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(CC2CN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)C2)c2cc(C3CC3)ccc21) `ZINC000568297490.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000568297490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000568297490 none CC1(C)CN(CC2CN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)C2)c2cc(C3CC3)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 1, 1, 1, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 4, 4, 4, 1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 47, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 16, 16, 4, 4, 4, 2, 2, 4, 4, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [8, 9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 636) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/636: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(CC2CN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)C2)c2cc(C3CC3)ccc21) `ZINC000568297490.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000568297490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000568297490 none CC1(C)CN(CC2CN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)C2)c2cc(C3CC3)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 1, 1, 1, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 15, 4, 4, 4, 1, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 4, 4, 4, 1, 1, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [43, 8, 9, 42, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 637) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/637: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(CC2CN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)C2)c2cc(C3CC3)ccc21) `ZINC000568297490.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000568297490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000568297490 none CC1(C)CN(CC2CN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)C2)c2cc(C3CC3)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 1, 1, 1, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 15, 4, 4, 4, 1, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 4, 4, 4, 1, 1, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [43, 8, 9, 42, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000568297490 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490 Building ZINC000568297490 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000568297490 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 634) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/634: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(CC2CN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)C2)c2cc(C3CC3)ccc21) `ZINC000568297490.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000568297490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000568297490 none CC1(C)CN(CC2CN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)C2)c2cc(C3CC3)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 1, 1, 1, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 4, 4, 4, 1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 47, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 16, 16, 4, 4, 4, 2, 2, 4, 4, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [8, 9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 635) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/635: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(CC2CN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)C2)c2cc(C3CC3)ccc21) `ZINC000568297490.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000568297490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000568297490 none CC1(C)CN(CC2CN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)C2)c2cc(C3CC3)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 1, 1, 1, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 4, 4, 4, 1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 47, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 16, 16, 4, 4, 4, 2, 2, 4, 4, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [8, 9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 636) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/636: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(CC2CN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)C2)c2cc(C3CC3)ccc21) `ZINC000568297490.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000568297490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000568297490 none CC1(C)CN(CC2CN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)C2)c2cc(C3CC3)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 1, 1, 1, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 15, 4, 4, 4, 1, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 4, 4, 4, 1, 1, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [43, 8, 9, 42, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 637) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/637: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(CC2CN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)C2)c2cc(C3CC3)ccc21) `ZINC000568297490.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000568297490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000568297490 none CC1(C)CN(CC2CN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)C2)c2cc(C3CC3)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 1, 1, 1, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 15, 4, 4, 4, 1, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 4, 4, 4, 1, 1, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [43, 8, 9, 42, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000568297490 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000568297490 Building ZINC000577237098 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000577237098 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 638) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/638 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/638' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccncc1)[C@H]1CCCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000577237098.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000577237098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000577237098 none O=C(N(Cc1ccncc1)[C@H]1CCCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 1, 1, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 8, 14, 19, 19, 15, 19, 19, 8, 16, 16, 16, 16, 16, 16, 31, 41, 41, 37, 41, 41, 16, 1, 1, 1, 2, 2, 1, 1, 2, 2, 14, 14, 19, 19, 19, 19, 16, 16, 16, 16, 16, 16, 31, 31, 41, 41, 41, 41, 41, 16, 16, 2, 2, 2, 2] 50 rigid atoms, others: [1, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 220 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 639) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/639 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/639' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccncc1)[C@H]1CCCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000577237098.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000577237098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000577237098 none O=C(N(Cc1ccncc1)[C@H]1CCCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 1, 1, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 8, 14, 19, 19, 15, 19, 19, 8, 16, 16, 16, 16, 16, 16, 31, 41, 41, 37, 41, 41, 16, 1, 1, 1, 2, 2, 1, 1, 2, 2, 14, 14, 19, 19, 19, 19, 16, 16, 16, 16, 16, 16, 31, 31, 41, 41, 41, 41, 41, 16, 16, 2, 2, 2, 2] 50 rigid atoms, others: [1, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 220 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 640) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/640 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/640' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccncc1)[C@H]1CCCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000577237098.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000577237098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000577237098 none O=C(N(Cc1ccncc1)[C@H]1CCCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 1, 1, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 8, 14, 19, 19, 18, 19, 19, 8, 15, 15, 15, 15, 15, 15, 30, 39, 39, 35, 39, 39, 15, 1, 1, 1, 2, 2, 1, 1, 2, 2, 14, 14, 19, 19, 19, 19, 15, 15, 15, 15, 15, 15, 30, 30, 39, 39, 39, 39, 39, 15, 15, 2, 2, 2, 2] 50 rigid atoms, others: [1, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 202 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 641) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/641 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/641' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccncc1)[C@H]1CCCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000577237098.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000577237098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000577237098 none O=C(N(Cc1ccncc1)[C@H]1CCCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 1, 1, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 8, 14, 19, 19, 18, 19, 19, 8, 15, 15, 15, 15, 15, 15, 30, 39, 39, 35, 39, 39, 15, 1, 1, 1, 2, 2, 1, 1, 2, 2, 14, 14, 19, 19, 19, 19, 15, 15, 15, 15, 15, 15, 30, 30, 39, 39, 39, 39, 39, 15, 15, 2, 2, 2, 2] 50 rigid atoms, others: [1, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 202 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000577237098 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098 Building ZINC000577237098 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000577237098 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 638) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/638: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccncc1)[C@H]1CCCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000577237098.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000577237098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000577237098 none O=C(N(Cc1ccncc1)[C@H]1CCCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 1, 1, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 8, 14, 19, 19, 15, 19, 19, 8, 16, 16, 16, 16, 16, 16, 31, 41, 41, 37, 41, 41, 16, 1, 1, 1, 2, 2, 1, 1, 2, 2, 14, 14, 19, 19, 19, 19, 16, 16, 16, 16, 16, 16, 31, 31, 41, 41, 41, 41, 41, 16, 16, 2, 2, 2, 2] 50 rigid atoms, others: [1, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 220 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 639) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/639: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccncc1)[C@H]1CCCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000577237098.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000577237098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000577237098 none O=C(N(Cc1ccncc1)[C@H]1CCCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 1, 1, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 8, 14, 19, 19, 15, 19, 19, 8, 16, 16, 16, 16, 16, 16, 31, 41, 41, 37, 41, 41, 16, 1, 1, 1, 2, 2, 1, 1, 2, 2, 14, 14, 19, 19, 19, 19, 16, 16, 16, 16, 16, 16, 31, 31, 41, 41, 41, 41, 41, 16, 16, 2, 2, 2, 2] 50 rigid atoms, others: [1, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 220 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 640) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/640: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccncc1)[C@H]1CCCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000577237098.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000577237098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000577237098 none O=C(N(Cc1ccncc1)[C@H]1CCCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 1, 1, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 8, 14, 19, 19, 18, 19, 19, 8, 15, 15, 15, 15, 15, 15, 30, 39, 39, 35, 39, 39, 15, 1, 1, 1, 2, 2, 1, 1, 2, 2, 14, 14, 19, 19, 19, 19, 15, 15, 15, 15, 15, 15, 30, 30, 39, 39, 39, 39, 39, 15, 15, 2, 2, 2, 2] 50 rigid atoms, others: [1, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 202 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 641) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/641: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccncc1)[C@H]1CCCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000577237098.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000577237098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000577237098 none O=C(N(Cc1ccncc1)[C@H]1CCCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 1, 1, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 8, 14, 19, 19, 18, 19, 19, 8, 15, 15, 15, 15, 15, 15, 30, 39, 39, 35, 39, 39, 15, 1, 1, 1, 2, 2, 1, 1, 2, 2, 14, 14, 19, 19, 19, 19, 15, 15, 15, 15, 15, 15, 30, 30, 39, 39, 39, 39, 39, 15, 15, 2, 2, 2, 2] 50 rigid atoms, others: [1, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 202 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000577237098 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098 Building ZINC000577237098 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000577237098 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 638) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/638: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccncc1)[C@H]1CCCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000577237098.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000577237098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000577237098 none O=C(N(Cc1ccncc1)[C@H]1CCCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 1, 1, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 8, 14, 19, 19, 15, 19, 19, 8, 16, 16, 16, 16, 16, 16, 31, 41, 41, 37, 41, 41, 16, 1, 1, 1, 2, 2, 1, 1, 2, 2, 14, 14, 19, 19, 19, 19, 16, 16, 16, 16, 16, 16, 31, 31, 41, 41, 41, 41, 41, 16, 16, 2, 2, 2, 2] 50 rigid atoms, others: [1, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 220 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 639) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/639: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccncc1)[C@H]1CCCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000577237098.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000577237098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000577237098 none O=C(N(Cc1ccncc1)[C@H]1CCCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 1, 1, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 8, 14, 19, 19, 15, 19, 19, 8, 16, 16, 16, 16, 16, 16, 31, 41, 41, 37, 41, 41, 16, 1, 1, 1, 2, 2, 1, 1, 2, 2, 14, 14, 19, 19, 19, 19, 16, 16, 16, 16, 16, 16, 31, 31, 41, 41, 41, 41, 41, 16, 16, 2, 2, 2, 2] 50 rigid atoms, others: [1, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 220 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 640) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/640: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccncc1)[C@H]1CCCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000577237098.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000577237098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000577237098 none O=C(N(Cc1ccncc1)[C@H]1CCCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 1, 1, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 8, 14, 19, 19, 18, 19, 19, 8, 15, 15, 15, 15, 15, 15, 30, 39, 39, 35, 39, 39, 15, 1, 1, 1, 2, 2, 1, 1, 2, 2, 14, 14, 19, 19, 19, 19, 15, 15, 15, 15, 15, 15, 30, 30, 39, 39, 39, 39, 39, 15, 15, 2, 2, 2, 2] 50 rigid atoms, others: [1, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 202 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 641) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/641: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccncc1)[C@H]1CCCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000577237098.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000577237098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000577237098 none O=C(N(Cc1ccncc1)[C@H]1CCCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 1, 1, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 8, 14, 19, 19, 18, 19, 19, 8, 15, 15, 15, 15, 15, 15, 30, 39, 39, 35, 39, 39, 15, 1, 1, 1, 2, 2, 1, 1, 2, 2, 14, 14, 19, 19, 19, 19, 15, 15, 15, 15, 15, 15, 30, 30, 39, 39, 39, 39, 39, 15, 15, 2, 2, 2, 2] 50 rigid atoms, others: [1, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 202 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000577237098 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098 Building ZINC000577237098 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000577237098 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 638) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/638: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccncc1)[C@H]1CCCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000577237098.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000577237098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000577237098 none O=C(N(Cc1ccncc1)[C@H]1CCCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 1, 1, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 8, 14, 19, 19, 15, 19, 19, 8, 16, 16, 16, 16, 16, 16, 31, 41, 41, 37, 41, 41, 16, 1, 1, 1, 2, 2, 1, 1, 2, 2, 14, 14, 19, 19, 19, 19, 16, 16, 16, 16, 16, 16, 31, 31, 41, 41, 41, 41, 41, 16, 16, 2, 2, 2, 2] 50 rigid atoms, others: [1, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 220 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 639) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/639: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccncc1)[C@H]1CCCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000577237098.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000577237098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000577237098 none O=C(N(Cc1ccncc1)[C@H]1CCCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 1, 1, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 8, 14, 19, 19, 15, 19, 19, 8, 16, 16, 16, 16, 16, 16, 31, 41, 41, 37, 41, 41, 16, 1, 1, 1, 2, 2, 1, 1, 2, 2, 14, 14, 19, 19, 19, 19, 16, 16, 16, 16, 16, 16, 31, 31, 41, 41, 41, 41, 41, 16, 16, 2, 2, 2, 2] 50 rigid atoms, others: [1, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 220 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 640) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/640: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccncc1)[C@H]1CCCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000577237098.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000577237098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000577237098 none O=C(N(Cc1ccncc1)[C@H]1CCCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 1, 1, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 8, 14, 19, 19, 18, 19, 19, 8, 15, 15, 15, 15, 15, 15, 30, 39, 39, 35, 39, 39, 15, 1, 1, 1, 2, 2, 1, 1, 2, 2, 14, 14, 19, 19, 19, 19, 15, 15, 15, 15, 15, 15, 30, 30, 39, 39, 39, 39, 39, 15, 15, 2, 2, 2, 2] 50 rigid atoms, others: [1, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 202 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 641) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/641: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccncc1)[C@H]1CCCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000577237098.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000577237098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000577237098 none O=C(N(Cc1ccncc1)[C@H]1CCCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 1, 1, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 8, 14, 19, 19, 18, 19, 19, 8, 15, 15, 15, 15, 15, 15, 30, 39, 39, 35, 39, 39, 15, 1, 1, 1, 2, 2, 1, 1, 2, 2, 14, 14, 19, 19, 19, 19, 15, 15, 15, 15, 15, 15, 30, 30, 39, 39, 39, 39, 39, 15, 15, 2, 2, 2, 2] 50 rigid atoms, others: [1, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 202 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000577237098 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237098 Building ZINC000577237099 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000577237099 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 642) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/642 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/642' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccncc1)[C@@H]1CCCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000577237099.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000577237099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000577237099 none O=C(N(Cc1ccncc1)[C@@H]1CCCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 1, 1, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 7, 11, 16, 16, 14, 16, 16, 10, 14, 14, 14, 14, 14, 14, 30, 42, 42, 30, 42, 42, 14, 1, 1, 1, 2, 2, 1, 1, 2, 2, 11, 11, 16, 16, 16, 16, 14, 14, 14, 14, 14, 14, 30, 30, 42, 42, 30, 42, 42, 14, 14, 2, 2, 2, 2] 50 rigid atoms, others: [1, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 212 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 643) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/643 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/643' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccncc1)[C@@H]1CCCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000577237099.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000577237099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000577237099 none O=C(N(Cc1ccncc1)[C@@H]1CCCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 1, 1, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 7, 11, 16, 16, 14, 16, 16, 10, 14, 14, 14, 14, 14, 14, 30, 42, 42, 30, 42, 42, 14, 1, 1, 1, 2, 2, 1, 1, 2, 2, 11, 11, 16, 16, 16, 16, 14, 14, 14, 14, 14, 14, 30, 30, 42, 42, 30, 42, 42, 14, 14, 2, 2, 2, 2] 50 rigid atoms, others: [1, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 212 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 644) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/644 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/644' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccncc1)[C@@H]1CCCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000577237099.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000577237099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000577237099 none O=C(N(Cc1ccncc1)[C@@H]1CCCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 1, 1, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 8, 14, 19, 19, 19, 19, 19, 10, 14, 14, 14, 14, 14, 14, 29, 41, 41, 41, 41, 41, 14, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 14, 19, 19, 19, 19, 14, 14, 14, 14, 14, 14, 29, 29, 41, 41, 41, 41, 41, 14, 14, 3, 3, 3, 3] 50 rigid atoms, others: [1, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 184 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 645) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/645 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/645' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccncc1)[C@@H]1CCCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000577237099.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000577237099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000577237099 none O=C(N(Cc1ccncc1)[C@@H]1CCCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 1, 1, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 8, 14, 19, 19, 19, 19, 19, 10, 14, 14, 14, 14, 14, 14, 29, 41, 41, 41, 41, 41, 14, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 14, 19, 19, 19, 19, 14, 14, 14, 14, 14, 14, 29, 29, 41, 41, 41, 41, 41, 14, 14, 3, 3, 3, 3] 50 rigid atoms, others: [1, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 184 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000577237099 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099 Building ZINC000577237099 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000577237099 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 642) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/642: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccncc1)[C@@H]1CCCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000577237099.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000577237099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000577237099 none O=C(N(Cc1ccncc1)[C@@H]1CCCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 1, 1, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 7, 11, 16, 16, 14, 16, 16, 10, 14, 14, 14, 14, 14, 14, 30, 42, 42, 30, 42, 42, 14, 1, 1, 1, 2, 2, 1, 1, 2, 2, 11, 11, 16, 16, 16, 16, 14, 14, 14, 14, 14, 14, 30, 30, 42, 42, 30, 42, 42, 14, 14, 2, 2, 2, 2] 50 rigid atoms, others: [1, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 212 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 643) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/643: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccncc1)[C@@H]1CCCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000577237099.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000577237099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000577237099 none O=C(N(Cc1ccncc1)[C@@H]1CCCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 1, 1, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 7, 11, 16, 16, 14, 16, 16, 10, 14, 14, 14, 14, 14, 14, 30, 42, 42, 30, 42, 42, 14, 1, 1, 1, 2, 2, 1, 1, 2, 2, 11, 11, 16, 16, 16, 16, 14, 14, 14, 14, 14, 14, 30, 30, 42, 42, 30, 42, 42, 14, 14, 2, 2, 2, 2] 50 rigid atoms, others: [1, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 212 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 644) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/644: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccncc1)[C@@H]1CCCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000577237099.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000577237099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000577237099 none O=C(N(Cc1ccncc1)[C@@H]1CCCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 1, 1, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 8, 14, 19, 19, 19, 19, 19, 10, 14, 14, 14, 14, 14, 14, 29, 41, 41, 41, 41, 41, 14, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 14, 19, 19, 19, 19, 14, 14, 14, 14, 14, 14, 29, 29, 41, 41, 41, 41, 41, 14, 14, 3, 3, 3, 3] 50 rigid atoms, others: [1, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 184 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 645) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/645: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccncc1)[C@@H]1CCCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000577237099.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000577237099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000577237099 none O=C(N(Cc1ccncc1)[C@@H]1CCCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 1, 1, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 8, 14, 19, 19, 19, 19, 19, 10, 14, 14, 14, 14, 14, 14, 29, 41, 41, 41, 41, 41, 14, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 14, 19, 19, 19, 19, 14, 14, 14, 14, 14, 14, 29, 29, 41, 41, 41, 41, 41, 14, 14, 3, 3, 3, 3] 50 rigid atoms, others: [1, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 184 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000577237099 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099 Building ZINC000577237099 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000577237099 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 642) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/642: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccncc1)[C@@H]1CCCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000577237099.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000577237099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000577237099 none O=C(N(Cc1ccncc1)[C@@H]1CCCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 1, 1, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 7, 11, 16, 16, 14, 16, 16, 10, 14, 14, 14, 14, 14, 14, 30, 42, 42, 30, 42, 42, 14, 1, 1, 1, 2, 2, 1, 1, 2, 2, 11, 11, 16, 16, 16, 16, 14, 14, 14, 14, 14, 14, 30, 30, 42, 42, 30, 42, 42, 14, 14, 2, 2, 2, 2] 50 rigid atoms, others: [1, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 212 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 643) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/643: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccncc1)[C@@H]1CCCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000577237099.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000577237099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000577237099 none O=C(N(Cc1ccncc1)[C@@H]1CCCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 1, 1, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 7, 11, 16, 16, 14, 16, 16, 10, 14, 14, 14, 14, 14, 14, 30, 42, 42, 30, 42, 42, 14, 1, 1, 1, 2, 2, 1, 1, 2, 2, 11, 11, 16, 16, 16, 16, 14, 14, 14, 14, 14, 14, 30, 30, 42, 42, 30, 42, 42, 14, 14, 2, 2, 2, 2] 50 rigid atoms, others: [1, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 212 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 644) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/644: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccncc1)[C@@H]1CCCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000577237099.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000577237099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000577237099 none O=C(N(Cc1ccncc1)[C@@H]1CCCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 1, 1, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 8, 14, 19, 19, 19, 19, 19, 10, 14, 14, 14, 14, 14, 14, 29, 41, 41, 41, 41, 41, 14, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 14, 19, 19, 19, 19, 14, 14, 14, 14, 14, 14, 29, 29, 41, 41, 41, 41, 41, 14, 14, 3, 3, 3, 3] 50 rigid atoms, others: [1, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 184 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 645) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/645: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccncc1)[C@@H]1CCCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000577237099.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000577237099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000577237099 none O=C(N(Cc1ccncc1)[C@@H]1CCCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 1, 1, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 8, 14, 19, 19, 19, 19, 19, 10, 14, 14, 14, 14, 14, 14, 29, 41, 41, 41, 41, 41, 14, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 14, 19, 19, 19, 19, 14, 14, 14, 14, 14, 14, 29, 29, 41, 41, 41, 41, 41, 14, 14, 3, 3, 3, 3] 50 rigid atoms, others: [1, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 184 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000577237099 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099 Building ZINC000577237099 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000577237099 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 642) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/642: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccncc1)[C@@H]1CCCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000577237099.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000577237099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000577237099 none O=C(N(Cc1ccncc1)[C@@H]1CCCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 1, 1, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 7, 11, 16, 16, 14, 16, 16, 10, 14, 14, 14, 14, 14, 14, 30, 42, 42, 30, 42, 42, 14, 1, 1, 1, 2, 2, 1, 1, 2, 2, 11, 11, 16, 16, 16, 16, 14, 14, 14, 14, 14, 14, 30, 30, 42, 42, 30, 42, 42, 14, 14, 2, 2, 2, 2] 50 rigid atoms, others: [1, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 212 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 643) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/643: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccncc1)[C@@H]1CCCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000577237099.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000577237099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000577237099 none O=C(N(Cc1ccncc1)[C@@H]1CCCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 1, 1, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 7, 11, 16, 16, 14, 16, 16, 10, 14, 14, 14, 14, 14, 14, 30, 42, 42, 30, 42, 42, 14, 1, 1, 1, 2, 2, 1, 1, 2, 2, 11, 11, 16, 16, 16, 16, 14, 14, 14, 14, 14, 14, 30, 30, 42, 42, 30, 42, 42, 14, 14, 2, 2, 2, 2] 50 rigid atoms, others: [1, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 212 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 644) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/644: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccncc1)[C@@H]1CCCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000577237099.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000577237099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000577237099 none O=C(N(Cc1ccncc1)[C@@H]1CCCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 1, 1, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 8, 14, 19, 19, 19, 19, 19, 10, 14, 14, 14, 14, 14, 14, 29, 41, 41, 41, 41, 41, 14, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 14, 19, 19, 19, 19, 14, 14, 14, 14, 14, 14, 29, 29, 41, 41, 41, 41, 41, 14, 14, 3, 3, 3, 3] 50 rigid atoms, others: [1, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 184 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 645) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/645: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccncc1)[C@@H]1CCCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000577237099.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000577237099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000577237099 none O=C(N(Cc1ccncc1)[C@@H]1CCCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 1, 1, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 8, 14, 19, 19, 19, 19, 19, 10, 14, 14, 14, 14, 14, 14, 29, 41, 41, 41, 41, 41, 14, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 14, 19, 19, 19, 19, 14, 14, 14, 14, 14, 14, 29, 29, 41, 41, 41, 41, 41, 14, 14, 3, 3, 3, 3] 50 rigid atoms, others: [1, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 184 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000577237099 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577237099 Building ZINC000577782387 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577782387' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577782387 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000577782387 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577782387/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577782387 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 646) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/646 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/646' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nnc(c2cccc(OC(F)(F)F)c2)s1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000577782387.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000577782387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577782387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000577782387 none O=C(Nc1nnc(c2cccc(OC(F)(F)F)c2)s1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 14, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 4, 4, 15, 15, 15, 15, 15, 50, 50, 50, 50, 15, 4, 1, 1, 1, 3, 3, 3, 3, 3, 2, 15, 15, 15, 15, 3, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577782387 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577782387/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577782387 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 647) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/647 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/647' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nnc(c2cccc(OC(F)(F)F)c2)s1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000577782387.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000577782387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577782387/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000577782387 none O=C(Nc1nnc(c2cccc(OC(F)(F)F)c2)s1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 14, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 4, 4, 15, 15, 15, 15, 15, 50, 50, 50, 50, 15, 4, 1, 1, 1, 3, 3, 3, 3, 3, 2, 15, 15, 15, 15, 3, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577782387 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000577782387 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577782387/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577782387/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577782387 Building ZINC000577782387 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577782387' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577782387 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000577782387 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577782387/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577782387 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 646) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/646: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nnc(c2cccc(OC(F)(F)F)c2)s1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000577782387.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000577782387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577782387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000577782387 none O=C(Nc1nnc(c2cccc(OC(F)(F)F)c2)s1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 14, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 4, 4, 15, 15, 15, 15, 15, 50, 50, 50, 50, 15, 4, 1, 1, 1, 3, 3, 3, 3, 3, 2, 15, 15, 15, 15, 3, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577782387 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577782387/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577782387 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 647) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/647: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nnc(c2cccc(OC(F)(F)F)c2)s1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000577782387.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000577782387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577782387/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000577782387 none O=C(Nc1nnc(c2cccc(OC(F)(F)F)c2)s1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 14, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 4, 4, 15, 15, 15, 15, 15, 50, 50, 50, 50, 15, 4, 1, 1, 1, 3, 3, 3, 3, 3, 2, 15, 15, 15, 15, 3, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577782387 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000577782387 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577782387/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577782387/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577782387 Building ZINC000577788636 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577788636' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577788636 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000577788636 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577788636/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577788636 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 648) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/648 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/648' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2nc3ccccc3n2C(C)C)cc1Cl) `ZINC000577788636.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000577788636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577788636/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000577788636 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2nc3ccccc3n2C(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 2, 5, 5, 1, 1, 1, 1, 6, 6, 12, 12, 12, 12, 12, 12, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 5, 5, 5, 10, 10, 10, 5, 5, 12, 12, 12, 12, 12, 12, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577788636 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577788636/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577788636 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 649) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/649 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/649' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2nc3ccccc3n2C(C)C)cc1Cl) `ZINC000577788636.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000577788636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577788636/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000577788636 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2nc3ccccc3n2C(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 7, 2, 7, 7, 1, 1, 1, 1, 6, 6, 10, 10, 10, 10, 10, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 7, 7, 7, 14, 14, 14, 7, 7, 10, 10, 10, 10, 10, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 7] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577788636 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000577788636 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577788636/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577788636/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577788636 Building ZINC000577788636 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577788636' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577788636 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000577788636 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577788636/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577788636 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 648) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/648: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2nc3ccccc3n2C(C)C)cc1Cl) `ZINC000577788636.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000577788636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577788636/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000577788636 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2nc3ccccc3n2C(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 2, 5, 5, 1, 1, 1, 1, 6, 6, 12, 12, 12, 12, 12, 12, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 5, 5, 5, 10, 10, 10, 5, 5, 12, 12, 12, 12, 12, 12, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577788636 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577788636/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577788636 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 649) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/649: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2nc3ccccc3n2C(C)C)cc1Cl) `ZINC000577788636.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000577788636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577788636/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000577788636 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2nc3ccccc3n2C(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 7, 2, 7, 7, 1, 1, 1, 1, 6, 6, 10, 10, 10, 10, 10, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 7, 7, 7, 14, 14, 14, 7, 7, 10, 10, 10, 10, 10, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 7] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577788636 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000577788636 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577788636/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577788636/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577788636 Building ZINC000577788637 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577788637' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577788637 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000577788637 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577788637/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577788637 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 650) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/650 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/650' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2nc3ccccc3n2C(C)C)cc1Cl) `ZINC000577788637.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000577788637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577788637/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000577788637 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2nc3ccccc3n2C(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 8, 8, 1, 1, 1, 1, 6, 6, 10, 10, 10, 10, 10, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 8, 8, 8, 14, 14, 14, 8, 8, 10, 10, 10, 10, 10, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 8] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577788637 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577788637/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577788637 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 651) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/651 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/651' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2nc3ccccc3n2C(C)C)cc1Cl) `ZINC000577788637.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000577788637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577788637/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000577788637 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2nc3ccccc3n2C(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 6, 6, 12, 12, 12, 12, 12, 12, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 6, 6, 11, 11, 11, 6, 6, 12, 12, 12, 12, 12, 12, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577788637 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000577788637 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577788637/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577788637/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577788637 Building ZINC000577788637 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577788637' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577788637 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000577788637 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577788637/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577788637 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 650) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/650: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2nc3ccccc3n2C(C)C)cc1Cl) `ZINC000577788637.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000577788637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577788637/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000577788637 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2nc3ccccc3n2C(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 8, 8, 1, 1, 1, 1, 6, 6, 10, 10, 10, 10, 10, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 8, 8, 8, 14, 14, 14, 8, 8, 10, 10, 10, 10, 10, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 8] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577788637 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577788637/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577788637 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 651) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/651: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2nc3ccccc3n2C(C)C)cc1Cl) `ZINC000577788637.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000577788637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577788637/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000577788637 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2nc3ccccc3n2C(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 6, 6, 12, 12, 12, 12, 12, 12, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 6, 6, 11, 11, 11, 6, 6, 12, 12, 12, 12, 12, 12, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577788637 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000577788637 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577788637/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577788637/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000577788637 Building ZINC000641908644 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000641908644' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000641908644 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000641908644 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000641908644/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000641908644 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 652) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/652 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/652' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1SCC(F)(F)F) `ZINC000641908644.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000641908644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000641908644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000641908644 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1SCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 14, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 5, 7, 7, 3, 3, 1, 1, 1, 1, 4, 4, 4, 8, 8, 6, 8, 8, 8, 15, 33, 33, 33, 33, 3, 3, 3, 7, 7, 6, 7, 7, 3, 3, 3, 4, 8, 8, 8, 8, 33, 33] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 136 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000641908644 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000641908644/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000641908644 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 653) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/653 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/653' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1SCC(F)(F)F) `ZINC000641908644.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000641908644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000641908644/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000641908644 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1SCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 14, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 4, 4, 4, 8, 8, 6, 8, 8, 8, 15, 33, 33, 33, 33, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 4, 8, 8, 8, 8, 33, 33] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 140 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000641908644 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000641908644 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000641908644/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000641908644/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000641908644 Building ZINC000641908644 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000641908644' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000641908644 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000641908644 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000641908644/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000641908644 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 652) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/652: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1SCC(F)(F)F) `ZINC000641908644.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000641908644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000641908644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000641908644 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1SCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 14, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 5, 7, 7, 3, 3, 1, 1, 1, 1, 4, 4, 4, 8, 8, 6, 8, 8, 8, 15, 33, 33, 33, 33, 3, 3, 3, 7, 7, 6, 7, 7, 3, 3, 3, 4, 8, 8, 8, 8, 33, 33] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 136 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000641908644 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000641908644/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000641908644 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 653) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/653: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1SCC(F)(F)F) `ZINC000641908644.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000641908644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000641908644/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000641908644 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1SCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 14, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 4, 4, 4, 8, 8, 6, 8, 8, 8, 15, 33, 33, 33, 33, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 4, 8, 8, 8, 8, 33, 33] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 140 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000641908644 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000641908644 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000641908644/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000641908644/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000641908644 Building ZINC000642018667 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642018667' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642018667 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000642018667 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642018667/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642018667 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 654) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/654 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/654' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)Cc1cccc(C)c1) `ZINC000642018667.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000642018667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642018667/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000642018667 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)Cc1cccc(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 3, 10, 10, 10, 10, 10, 10, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 6, 11, 11, 11, 11, 11, 11, 3, 3, 3, 10, 10, 3, 10, 3, 3, 3, 3, 3, 3, 6, 6, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642018667 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642018667/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642018667 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 655) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/655 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/655' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)Cc1cccc(C)c1) `ZINC000642018667.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000642018667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642018667/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000642018667 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)Cc1cccc(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 9, 9, 9, 9, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 6, 13, 13, 6, 13, 13, 13, 3, 3, 3, 9, 9, 3, 9, 3, 3, 3, 3, 3, 3, 6, 6, 13, 13, 6, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642018667 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000642018667 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642018667/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642018667/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642018667 Building ZINC000642018667 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642018667' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642018667 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000642018667 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642018667/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642018667 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 654) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/654: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)Cc1cccc(C)c1) `ZINC000642018667.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000642018667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642018667/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000642018667 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)Cc1cccc(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 3, 10, 10, 10, 10, 10, 10, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 6, 11, 11, 11, 11, 11, 11, 3, 3, 3, 10, 10, 3, 10, 3, 3, 3, 3, 3, 3, 6, 6, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642018667 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642018667/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642018667 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 655) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/655: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)Cc1cccc(C)c1) `ZINC000642018667.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000642018667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642018667/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000642018667 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)Cc1cccc(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 9, 9, 9, 9, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 6, 13, 13, 6, 13, 13, 13, 3, 3, 3, 9, 9, 3, 9, 3, 3, 3, 3, 3, 3, 6, 6, 13, 13, 6, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642018667 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000642018667 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642018667/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642018667/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642018667 Building ZINC000642071668 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642071668' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642071668 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000642071668 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642071668/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642071668 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 656) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/656 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/656' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(Cc1ccc(F)cc1F)C1CCCC1) `ZINC000642071668.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000642071668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642071668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000642071668 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(Cc1ccc(F)cc1F)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 15, 1, 1, 15, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 1, 1, 1, 1, 5, 5, 8, 13, 18, 18, 18, 18, 18, 18, 18, 8, 13, 13, 13, 13, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 3, 13, 13, 18, 18, 18, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 95 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642071668 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642071668/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642071668 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 657) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/657 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/657' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(Cc1ccc(F)cc1F)C1CCCC1) `ZINC000642071668.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000642071668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642071668/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000642071668 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(Cc1ccc(F)cc1F)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 15, 1, 1, 15, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 3, 11, 11, 3, 3, 1, 1, 1, 1, 5, 5, 8, 13, 20, 20, 17, 20, 20, 20, 20, 8, 14, 14, 14, 14, 3, 3, 3, 11, 11, 6, 11, 11, 3, 3, 3, 13, 13, 20, 20, 20, 14, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 130 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642071668 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000642071668 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642071668/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642071668/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642071668 Building ZINC000642071668 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642071668' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642071668 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000642071668 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642071668/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642071668 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 656) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/656: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(Cc1ccc(F)cc1F)C1CCCC1) `ZINC000642071668.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000642071668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642071668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000642071668 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(Cc1ccc(F)cc1F)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 15, 1, 1, 15, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 1, 1, 1, 1, 5, 5, 8, 13, 18, 18, 18, 18, 18, 18, 18, 8, 13, 13, 13, 13, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 3, 13, 13, 18, 18, 18, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 95 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642071668 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642071668/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642071668 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 657) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/657: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(Cc1ccc(F)cc1F)C1CCCC1) `ZINC000642071668.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000642071668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642071668/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000642071668 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(Cc1ccc(F)cc1F)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 15, 1, 1, 15, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 3, 11, 11, 3, 3, 1, 1, 1, 1, 5, 5, 8, 13, 20, 20, 17, 20, 20, 20, 20, 8, 14, 14, 14, 14, 3, 3, 3, 11, 11, 6, 11, 11, 3, 3, 3, 13, 13, 20, 20, 20, 14, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 130 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642071668 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000642071668 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642071668/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642071668/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642071668 Building ZINC000642075380 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642075380' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642075380 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000642075380 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642075380/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642075380 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 658) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/658 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/658' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(CCc1ccccc1F)C1CCCC1) `ZINC000642075380.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000642075380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642075380/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000642075380 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(CCc1ccccc1F)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 15, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 2, 2, 3, 9, 10, 28, 28, 16, 28, 28, 28, 4, 9, 9, 9, 9, 3, 3, 3, 7, 7, 5, 7, 7, 3, 3, 3, 9, 9, 10, 10, 28, 28, 28, 28, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 151 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642075380 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642075380/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642075380 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 659) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/659 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/659' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(CCc1ccccc1F)C1CCCC1) `ZINC000642075380.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000642075380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642075380/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000642075380 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(CCc1ccccc1F)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 15, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 3, 9, 10, 29, 29, 18, 29, 29, 29, 4, 8, 8, 8, 8, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 9, 9, 10, 10, 29, 29, 29, 29, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 140 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642075380 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000642075380 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642075380/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642075380/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642075380 Building ZINC000642075380 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642075380' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642075380 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000642075380 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642075380/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642075380 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 658) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/658: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(CCc1ccccc1F)C1CCCC1) `ZINC000642075380.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000642075380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642075380/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000642075380 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(CCc1ccccc1F)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 15, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 2, 2, 3, 9, 10, 28, 28, 16, 28, 28, 28, 4, 9, 9, 9, 9, 3, 3, 3, 7, 7, 5, 7, 7, 3, 3, 3, 9, 9, 10, 10, 28, 28, 28, 28, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 151 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642075380 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642075380/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642075380 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 659) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/659: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(CCc1ccccc1F)C1CCCC1) `ZINC000642075380.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000642075380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642075380/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000642075380 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(CCc1ccccc1F)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 15, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 3, 9, 10, 29, 29, 18, 29, 29, 29, 4, 8, 8, 8, 8, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 9, 9, 10, 10, 29, 29, 29, 29, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 140 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642075380 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000642075380 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642075380/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642075380/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642075380 Building ZINC000642232655 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642232655' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642232655 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000642232655 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642232655/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642232655 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 660) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/660 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/660' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1OCC(C)C) `ZINC000642232655.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000642232655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642232655/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000642232655 none COc1cc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1OCC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 6, 6, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 6, 6, 6, 6, 28, 37, 40, 42, 12, 12, 12, 6, 2, 2, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 6, 6, 37, 37, 42, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642232655 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642232655/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642232655 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 661) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/661 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/661' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1OCC(C)C) `ZINC000642232655.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000642232655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642232655/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000642232655 none COc1cc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1OCC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 7, 7, 7, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 7, 7, 7, 7, 22, 30, 43, 44, 14, 14, 14, 7, 3, 3, 3, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 7, 7, 30, 30, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642232655 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000642232655 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642232655/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642232655/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642232655 Building ZINC000642232655 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642232655' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642232655 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000642232655 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642232655/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642232655 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 660) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/660: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1OCC(C)C) `ZINC000642232655.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000642232655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642232655/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000642232655 none COc1cc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1OCC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 6, 6, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 6, 6, 6, 6, 28, 37, 40, 42, 12, 12, 12, 6, 2, 2, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 6, 6, 37, 37, 42, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642232655 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642232655/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642232655 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 661) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/661: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1OCC(C)C) `ZINC000642232655.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000642232655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642232655/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000642232655 none COc1cc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1OCC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 7, 7, 7, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 7, 7, 7, 7, 22, 30, 43, 44, 14, 14, 14, 7, 3, 3, 3, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 7, 7, 30, 30, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642232655 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000642232655 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642232655/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642232655/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642232655 Building ZINC000642232656 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642232656' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642232656 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000642232656 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642232656/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642232656 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 662) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/662 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/662' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1OCC(C)C) `ZINC000642232656.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000642232656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642232656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000642232656 none COc1cc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1OCC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 7, 7, 7, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 7, 7, 7, 7, 21, 33, 40, 44, 14, 14, 14, 7, 3, 3, 3, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 7, 7, 33, 33, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642232656 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642232656/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642232656 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 663) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/663 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/663' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1OCC(C)C) `ZINC000642232656.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000642232656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642232656/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000642232656 none COc1cc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1OCC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 7, 7, 7, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 7, 7, 7, 7, 28, 37, 44, 46, 12, 12, 12, 7, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 7, 7, 37, 37, 46, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642232656 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000642232656 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642232656/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642232656/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642232656 Building ZINC000642232656 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642232656' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642232656 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000642232656 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642232656/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642232656 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 662) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/662: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1OCC(C)C) `ZINC000642232656.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000642232656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642232656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000642232656 none COc1cc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1OCC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 7, 7, 7, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 7, 7, 7, 7, 21, 33, 40, 44, 14, 14, 14, 7, 3, 3, 3, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 7, 7, 33, 33, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642232656 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642232656/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642232656 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 663) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/663: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1OCC(C)C) `ZINC000642232656.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000642232656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642232656/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000642232656 none COc1cc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1OCC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 7, 7, 7, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 7, 7, 7, 7, 28, 37, 44, 46, 12, 12, 12, 7, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 7, 7, 37, 37, 46, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642232656 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000642232656 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642232656/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642232656/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642232656 Building ZINC000642606093 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642606093' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642606093 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000642606093 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642606093/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642606093 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 664) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/664 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/664' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC=C(c2c[nH]c3cc(C)ccc32)CC1) `ZINC000642606093.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000642606093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642606093/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000642606093 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC=C(c2c[nH]c3cc(C)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 6, 1, 1, 1, 5, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 4, 8, 8, 2, 2, 1, 1, 1, 2, 4, 7, 7, 7, 7, 7, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 7, 7, 2, 2, 2, 8, 8, 4, 8, 8, 2, 2, 2, 7, 7, 7, 29, 29, 29, 29, 29, 29, 29, 7, 7, 7, 7] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 65 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642606093 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642606093/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642606093 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 665) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/665 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/665' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC=C(c2c[nH]c3cc(C)ccc32)CC1) `ZINC000642606093.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000642606093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642606093/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000642606093 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC=C(c2c[nH]c3cc(C)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 6, 1, 1, 1, 5, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 2, 2, 1, 1, 1, 2, 4, 7, 7, 7, 7, 7, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 7, 7, 2, 2, 2, 8, 8, 2, 8, 8, 2, 2, 2, 7, 7, 7, 30, 30, 30, 30, 30, 30, 30, 7, 7, 7, 7] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 64 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642606093 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000642606093 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642606093/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642606093/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642606093 Building ZINC000642606093 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642606093' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642606093 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000642606093 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642606093/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642606093 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 664) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/664: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC=C(c2c[nH]c3cc(C)ccc32)CC1) `ZINC000642606093.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000642606093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642606093/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000642606093 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC=C(c2c[nH]c3cc(C)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 6, 1, 1, 1, 5, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 4, 8, 8, 2, 2, 1, 1, 1, 2, 4, 7, 7, 7, 7, 7, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 7, 7, 2, 2, 2, 8, 8, 4, 8, 8, 2, 2, 2, 7, 7, 7, 29, 29, 29, 29, 29, 29, 29, 7, 7, 7, 7] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 65 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642606093 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642606093/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642606093 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 665) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/665: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC=C(c2c[nH]c3cc(C)ccc32)CC1) `ZINC000642606093.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000642606093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642606093/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000642606093 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC=C(c2c[nH]c3cc(C)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 6, 1, 1, 1, 5, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 2, 2, 1, 1, 1, 2, 4, 7, 7, 7, 7, 7, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 7, 7, 2, 2, 2, 8, 8, 2, 8, 8, 2, 2, 2, 7, 7, 7, 30, 30, 30, 30, 30, 30, 30, 7, 7, 7, 7] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 64 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642606093 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000642606093 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642606093/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642606093/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000642606093 Building ZINC000643173933 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000643173933' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000643173933 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000643173933 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000643173933/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000643173933 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 666) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/666 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/666' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(CC(F)(F)F)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000643173933.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000643173933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000643173933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000643173933 none CCCCN(CC(F)(F)F)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 5, 15, 15, 15, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 2, 1, 2, 4, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 10, 10, 10, 10, 10, 7, 7, 5, 5, 4, 4, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2] 50 rigid atoms, others: [4, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000643173933 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000643173933/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000643173933 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 667) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/667 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/667' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(CC(F)(F)F)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000643173933.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000643173933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000643173933/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000643173933 none CCCCN(CC(F)(F)F)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 5, 15, 15, 15, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 2, 1, 2, 4, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 11, 11, 2, 11, 11, 11, 11, 11, 11, 2, 2, 10, 10, 10, 10, 10, 7, 7, 5, 5, 4, 4, 2, 2, 2, 11, 11, 2, 11, 2, 2, 2] 50 rigid atoms, others: [4, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000643173933 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000643173933 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000643173933/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000643173933/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000643173933 Building ZINC000643173933 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000643173933' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000643173933 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000643173933 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000643173933/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000643173933 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 666) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/666: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(CC(F)(F)F)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000643173933.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000643173933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000643173933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000643173933 none CCCCN(CC(F)(F)F)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 5, 15, 15, 15, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 2, 1, 2, 4, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 10, 10, 10, 10, 10, 7, 7, 5, 5, 4, 4, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2] 50 rigid atoms, others: [4, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000643173933 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000643173933/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000643173933 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 667) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/667: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(CC(F)(F)F)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000643173933.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000643173933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000643173933/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000643173933 none CCCCN(CC(F)(F)F)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 5, 15, 15, 15, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 2, 1, 2, 4, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 11, 11, 2, 11, 11, 11, 11, 11, 11, 2, 2, 10, 10, 10, 10, 10, 7, 7, 5, 5, 4, 4, 2, 2, 2, 11, 11, 2, 11, 2, 2, 2] 50 rigid atoms, others: [4, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000643173933 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000643173933 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000643173933/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000643173933/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000643173933 Building ZINC000643185115 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000643185115' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000643185115 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000643185115 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000643185115/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000643185115 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 668) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/668 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/668' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(CC(C)C)CC(F)(F)F) `ZINC000643185115.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000643185115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000643185115/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000643185115 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(CC(C)C)CC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 22, 22, 3, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 1, 3, 3, 5, 6, 7, 7, 5, 7, 7, 7, 7, 3, 3, 3, 22, 22, 3, 22, 3, 3, 3, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 86 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000643185115 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000643185115/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000643185115 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 669) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/669 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/669' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(CC(C)C)CC(F)(F)F) `ZINC000643185115.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000643185115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000643185115/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000643185115 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(CC(C)C)CC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 16, 16, 2, 16, 16, 16, 16, 16, 16, 2, 2, 1, 1, 1, 1, 4, 4, 7, 9, 9, 9, 7, 10, 10, 10, 10, 2, 2, 2, 16, 16, 2, 16, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 81 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000643185115 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000643185115 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000643185115/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000643185115/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000643185115 Building ZINC000643185115 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000643185115' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000643185115 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000643185115 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000643185115/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000643185115 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 668) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/668: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(CC(C)C)CC(F)(F)F) `ZINC000643185115.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000643185115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000643185115/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000643185115 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(CC(C)C)CC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 22, 22, 3, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 1, 3, 3, 5, 6, 7, 7, 5, 7, 7, 7, 7, 3, 3, 3, 22, 22, 3, 22, 3, 3, 3, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 86 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000643185115 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000643185115/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000643185115 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 669) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/669: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(CC(C)C)CC(F)(F)F) `ZINC000643185115.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000643185115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000643185115/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000643185115 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(CC(C)C)CC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 16, 16, 2, 16, 16, 16, 16, 16, 16, 2, 2, 1, 1, 1, 1, 4, 4, 7, 9, 9, 9, 7, 10, 10, 10, 10, 2, 2, 2, 16, 16, 2, 16, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 81 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000643185115 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000643185115 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000643185115/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000643185115/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000643185115 Building ZINC000646778410 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000646778410' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000646778410 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000646778410 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000646778410/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000646778410 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 670) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/670 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/670' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(Cc1ccccc1)c1nc2ccc(Cl)cc2s1) `ZINC000646778410.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000646778410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000646778410/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000646778410 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(Cc1ccccc1)c1nc2ccc(Cl)cc2s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 16, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 7, 18, 25, 25, 22, 25, 25, 7, 30, 30, 30, 30, 30, 30, 30, 30, 29, 3, 3, 3, 3, 3, 3, 3, 3, 3, 18, 18, 25, 25, 25, 25, 25, 30, 30, 30] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 128 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000646778410 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000646778410/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000646778410 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 671) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/671 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/671' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(Cc1ccccc1)c1nc2ccc(Cl)cc2s1) `ZINC000646778410.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000646778410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000646778410/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000646778410 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(Cc1ccccc1)c1nc2ccc(Cl)cc2s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 16, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 7, 18, 25, 25, 20, 25, 25, 7, 30, 30, 30, 30, 30, 30, 30, 30, 29, 3, 3, 3, 3, 3, 3, 3, 3, 3, 18, 18, 25, 25, 25, 25, 25, 30, 30, 30] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 139 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000646778410 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000646778410 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000646778410/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000646778410/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000646778410 Building ZINC000646778410 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000646778410' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000646778410 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000646778410 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000646778410/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000646778410 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 670) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/670: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(Cc1ccccc1)c1nc2ccc(Cl)cc2s1) `ZINC000646778410.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000646778410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000646778410/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000646778410 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(Cc1ccccc1)c1nc2ccc(Cl)cc2s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 16, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 7, 18, 25, 25, 22, 25, 25, 7, 30, 30, 30, 30, 30, 30, 30, 30, 29, 3, 3, 3, 3, 3, 3, 3, 3, 3, 18, 18, 25, 25, 25, 25, 25, 30, 30, 30] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 128 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000646778410 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000646778410/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000646778410 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 671) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/671: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(Cc1ccccc1)c1nc2ccc(Cl)cc2s1) `ZINC000646778410.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000646778410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000646778410/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000646778410 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(Cc1ccccc1)c1nc2ccc(Cl)cc2s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 16, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 7, 18, 25, 25, 20, 25, 25, 7, 30, 30, 30, 30, 30, 30, 30, 30, 29, 3, 3, 3, 3, 3, 3, 3, 3, 3, 18, 18, 25, 25, 25, 25, 25, 30, 30, 30] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 139 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000646778410 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000646778410 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000646778410/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000646778410/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000646778410 Building ZINC000648035331 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648035331' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648035331 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648035331 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648035331/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648035331 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 672) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/672 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/672' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(F)c(F)c1F) `ZINC000648035331.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648035331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648035331/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000648035331 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(F)c(F)c1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 15, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 20, 20, 3, 20, 20, 20, 20, 20, 20, 3, 3, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 20, 20, 4, 20, 3, 3, 3, 3, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 64 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648035331 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648035331/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648035331 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 673) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/673 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/673' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(F)c(F)c1F) `ZINC000648035331.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648035331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648035331/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000648035331 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(F)c(F)c1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 15, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 22, 22, 4, 22, 22, 22, 22, 22, 22, 4, 4, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 4, 4, 4, 22, 22, 4, 22, 4, 4, 4, 3, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 63 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648035331 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000648035331 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648035331/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648035331/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648035331 Building ZINC000648035331 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648035331' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648035331 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648035331 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648035331/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648035331 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 672) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/672: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(F)c(F)c1F) `ZINC000648035331.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648035331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648035331/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000648035331 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(F)c(F)c1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 15, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 20, 20, 3, 20, 20, 20, 20, 20, 20, 3, 3, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 20, 20, 4, 20, 3, 3, 3, 3, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 64 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648035331 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648035331/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648035331 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 673) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/673: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(F)c(F)c1F) `ZINC000648035331.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648035331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648035331/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000648035331 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(F)c(F)c1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 15, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 22, 22, 4, 22, 22, 22, 22, 22, 22, 4, 4, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 4, 4, 4, 22, 22, 4, 22, 4, 4, 4, 3, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 63 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648035331 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000648035331 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648035331/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648035331/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648035331 Building ZINC000648035309 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648035309' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648035309 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648035309 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648035309/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648035309 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 674) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/674 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/674' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1c1nc2ccccc2[nH]1) `ZINC000648035309.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648035309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648035309/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000648035309 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1c1nc2ccccc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 12, 12, 4, 12, 12, 4, 4, 1, 1, 1, 1, 6, 6, 6, 17, 17, 10, 17, 17, 17, 22, 22, 22, 22, 22, 22, 22, 22, 22, 4, 4, 4, 12, 12, 5, 12, 12, 4, 4, 4, 6, 17, 17, 17, 17, 22, 22, 22, 22] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 98 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648035309 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648035309/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648035309 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 675) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/675 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/675' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1c1nc2ccccc2[nH]1) `ZINC000648035309.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648035309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648035309/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000648035309 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1c1nc2ccccc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 12, 12, 4, 12, 12, 4, 4, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 17, 17, 17, 22, 22, 22, 22, 22, 22, 22, 22, 22, 4, 4, 4, 12, 12, 4, 12, 12, 4, 4, 4, 6, 17, 17, 17, 17, 22, 22, 22, 22] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 67 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648035309 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000648035309 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648035309/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648035309/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648035309 Building ZINC000648035309 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648035309' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648035309 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648035309 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648035309/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648035309 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 674) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/674: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1c1nc2ccccc2[nH]1) `ZINC000648035309.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648035309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648035309/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000648035309 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1c1nc2ccccc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 12, 12, 4, 12, 12, 4, 4, 1, 1, 1, 1, 6, 6, 6, 17, 17, 10, 17, 17, 17, 22, 22, 22, 22, 22, 22, 22, 22, 22, 4, 4, 4, 12, 12, 5, 12, 12, 4, 4, 4, 6, 17, 17, 17, 17, 22, 22, 22, 22] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 98 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648035309 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648035309/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648035309 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 675) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/675: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1c1nc2ccccc2[nH]1) `ZINC000648035309.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648035309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648035309/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000648035309 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1c1nc2ccccc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 12, 12, 4, 12, 12, 4, 4, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 17, 17, 17, 22, 22, 22, 22, 22, 22, 22, 22, 22, 4, 4, 4, 12, 12, 4, 12, 12, 4, 4, 4, 6, 17, 17, 17, 17, 22, 22, 22, 22] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 67 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648035309 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000648035309 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648035309/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648035309/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648035309 Building ZINC000648039979 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648039979' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648039979 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648039979 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648039979/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648039979 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 676) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/676 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/676' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000648039979.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648039979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648039979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000648039979 none CC(=O)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', '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, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 10, 5, 5, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 10, 10, 10, 5, 5, 5, 5, 2, 2, 2, 2, 10, 10, 4, 10, 2, 2, 2] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648039979 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648039979/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648039979 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 677) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/677 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/677' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000648039979.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648039979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648039979/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000648039979 none CC(=O)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', '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, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 11, 11, 11, 6, 6, 6, 6, 2, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648039979 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000648039979 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648039979/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648039979/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648039979 Building ZINC000648039979 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648039979' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648039979 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648039979 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648039979/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648039979 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 676) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/676: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000648039979.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648039979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648039979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000648039979 none CC(=O)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', '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, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 10, 5, 5, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 10, 10, 10, 5, 5, 5, 5, 2, 2, 2, 2, 10, 10, 4, 10, 2, 2, 2] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648039979 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648039979/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648039979 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 677) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/677: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000648039979.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648039979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648039979/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000648039979 none CC(=O)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', '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, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 11, 11, 11, 6, 6, 6, 6, 2, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648039979 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000648039979 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648039979/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648039979/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648039979 Building ZINC000648049223 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648049223' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648049223 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648049223 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648049223/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648049223 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 678) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/678 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/678' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)c1sc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)nc1c1ccccc1) `ZINC000648049223.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648049223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648049223/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000648049223 none CC(=O)c1sc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)nc1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'C.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'] dock atom type numbers: [5, 1, 11, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 25, 4, 4, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 4, 4, 4, 13, 13, 6, 13, 13, 25, 25, 25, 2, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 13, 13, 8, 13, 13] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 102 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648049223 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648049223/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648049223 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 679) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/679 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/679' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)c1sc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)nc1c1ccccc1) `ZINC000648049223.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648049223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648049223/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000648049223 none CC(=O)c1sc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)nc1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'C.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'] dock atom type numbers: [5, 1, 11, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 25, 4, 4, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 4, 4, 4, 12, 12, 4, 12, 12, 25, 25, 25, 2, 3, 3, 3, 7, 7, 5, 7, 7, 3, 3, 3, 12, 12, 8, 12, 12] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 116 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648049223 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000648049223 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648049223/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648049223/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648049223 Building ZINC000648049223 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648049223' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648049223 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648049223 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648049223/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648049223 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 678) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/678: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)c1sc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)nc1c1ccccc1) `ZINC000648049223.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648049223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648049223/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000648049223 none CC(=O)c1sc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)nc1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'C.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'] dock atom type numbers: [5, 1, 11, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 25, 4, 4, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 4, 4, 4, 13, 13, 6, 13, 13, 25, 25, 25, 2, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 13, 13, 8, 13, 13] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 102 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648049223 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648049223/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648049223 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 679) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/679: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)c1sc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)nc1c1ccccc1) `ZINC000648049223.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648049223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648049223/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000648049223 none CC(=O)c1sc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)nc1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'C.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'] dock atom type numbers: [5, 1, 11, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 25, 4, 4, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 4, 4, 4, 12, 12, 4, 12, 12, 25, 25, 25, 2, 3, 3, 3, 7, 7, 5, 7, 7, 3, 3, 3, 12, 12, 8, 12, 12] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 116 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648049223 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000648049223 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648049223/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648049223/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648049223 Building ZINC000648634516 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648634516' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648634516 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648634516 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648634516/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648634516 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 680) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/680 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/680' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc2nc(N3CCCC3)sc2c1) `ZINC000648634516.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648634516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648634516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000648634516 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc2nc(N3CCCC3)sc2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 12, 12, 4, 12, 12, 4, 4, 1, 1, 1, 1, 5, 5, 5, 25, 25, 25, 25, 25, 25, 28, 28, 28, 28, 25, 25, 25, 4, 4, 4, 12, 12, 4, 12, 12, 4, 4, 4, 5, 25, 25, 28, 28, 28, 28, 28, 28, 28, 28, 25] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 73 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648634516 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648634516/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648634516 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 681) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/681 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/681' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc2nc(N3CCCC3)sc2c1) `ZINC000648634516.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648634516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648634516/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000648634516 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc2nc(N3CCCC3)sc2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 10, 10, 4, 10, 10, 4, 4, 1, 1, 1, 1, 5, 5, 5, 28, 28, 28, 28, 28, 28, 31, 31, 31, 31, 28, 28, 28, 4, 4, 4, 10, 10, 4, 10, 10, 4, 4, 4, 5, 28, 28, 31, 31, 31, 31, 31, 31, 31, 31, 28] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 70 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648634516 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000648634516 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648634516/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648634516/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648634516 Building ZINC000648634516 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648634516' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648634516 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648634516 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648634516/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648634516 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 680) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/680: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc2nc(N3CCCC3)sc2c1) `ZINC000648634516.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648634516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648634516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000648634516 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc2nc(N3CCCC3)sc2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 12, 12, 4, 12, 12, 4, 4, 1, 1, 1, 1, 5, 5, 5, 25, 25, 25, 25, 25, 25, 28, 28, 28, 28, 25, 25, 25, 4, 4, 4, 12, 12, 4, 12, 12, 4, 4, 4, 5, 25, 25, 28, 28, 28, 28, 28, 28, 28, 28, 25] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 73 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648634516 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648634516/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648634516 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 681) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/681: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc2nc(N3CCCC3)sc2c1) `ZINC000648634516.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648634516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648634516/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000648634516 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc2nc(N3CCCC3)sc2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 10, 10, 4, 10, 10, 4, 4, 1, 1, 1, 1, 5, 5, 5, 28, 28, 28, 28, 28, 28, 31, 31, 31, 31, 28, 28, 28, 4, 4, 4, 10, 10, 4, 10, 10, 4, 4, 4, 5, 28, 28, 31, 31, 31, 31, 31, 31, 31, 31, 28] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 70 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648634516 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000648634516 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648634516/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648634516/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648634516 Building ZINC000648879673 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648879673' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648879673 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648879673 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648879673/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648879673 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 682) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/682 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/682' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(c2cc(C)c(C)cc2C)nn1c1ccccc1) `ZINC000648879673.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648879673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648879673/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000648879673 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(c2cc(C)c(C)cc2C)nn1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 5, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 6, 10, 10, 10, 38, 38, 38, 10, 10, 38, 38, 38, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 10, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 10, 10, 10, 10, 10] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648879673 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648879673/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648879673 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 683) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/683 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/683' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(c2cc(C)c(C)cc2C)nn1c1ccccc1) `ZINC000648879673.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648879673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648879673/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000648879673 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(c2cc(C)c(C)cc2C)nn1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 5, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 6, 10, 10, 10, 38, 38, 38, 30, 38, 38, 38, 38, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 10, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 10, 10, 10, 10, 10] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648879673 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000648879673 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648879673/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648879673/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648879673 Building ZINC000648879673 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648879673' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648879673 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648879673 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648879673/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648879673 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 682) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/682: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(c2cc(C)c(C)cc2C)nn1c1ccccc1) `ZINC000648879673.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648879673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648879673/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000648879673 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(c2cc(C)c(C)cc2C)nn1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 5, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 6, 10, 10, 10, 38, 38, 38, 10, 10, 38, 38, 38, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 10, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 10, 10, 10, 10, 10] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648879673 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648879673/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648879673 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 683) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/683: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(c2cc(C)c(C)cc2C)nn1c1ccccc1) `ZINC000648879673.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648879673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648879673/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000648879673 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(c2cc(C)c(C)cc2C)nn1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 5, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 6, 10, 10, 10, 38, 38, 38, 30, 38, 38, 38, 38, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 10, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 10, 10, 10, 10, 10] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648879673 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000648879673 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648879673/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648879673/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000648879673 Building ZINC001276376766 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276376766' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276376766 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001276376766 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276376766/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276376766 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 684) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/684 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/684' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1csnc1c1cccc(C(F)(F)F)c1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001276376766.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001276376766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276376766/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001276376766 none O=C(Nc1csnc1c1cccc(C(F)(F)F)c1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'S.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 14, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 6, 6, 6, 25, 25, 10, 25, 25, 25, 25, 25, 25, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 6, 25, 25, 10, 25, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276376766 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276376766/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276376766 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 685) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/685 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/685' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1csnc1c1cccc(C(F)(F)F)c1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001276376766.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001276376766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276376766/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001276376766 none O=C(Nc1csnc1c1cccc(C(F)(F)F)c1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'S.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 14, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 6, 6, 6, 25, 25, 10, 25, 25, 25, 25, 25, 25, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 6, 25, 25, 25, 25, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276376766 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001276376766 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276376766/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276376766/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276376766 Building ZINC001276376766 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276376766' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276376766 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001276376766 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276376766/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276376766 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 684) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/684: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1csnc1c1cccc(C(F)(F)F)c1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001276376766.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001276376766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276376766/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001276376766 none O=C(Nc1csnc1c1cccc(C(F)(F)F)c1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'S.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 14, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 6, 6, 6, 25, 25, 10, 25, 25, 25, 25, 25, 25, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 6, 25, 25, 10, 25, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276376766 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276376766/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276376766 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 685) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/685: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1csnc1c1cccc(C(F)(F)F)c1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001276376766.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001276376766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276376766/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001276376766 none O=C(Nc1csnc1c1cccc(C(F)(F)F)c1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'S.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 14, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 6, 6, 6, 25, 25, 10, 25, 25, 25, 25, 25, 25, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 6, 25, 25, 25, 25, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276376766 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001276376766 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276376766/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276376766/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276376766 Building ZINC000677168516 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000677168516' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000677168516 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000677168516 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000677168516/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000677168516 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 686) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/686 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/686' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(SCc2ccccc2)cn1) `ZINC000677168516.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000677168516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000677168516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000677168516 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(SCc2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 5, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 20, 43, 45, 45, 45, 45, 45, 5, 5, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 3, 5, 5, 43, 43, 45, 45, 45, 45, 45, 5] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 160 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000677168516 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000677168516/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000677168516 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 687) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/687 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/687' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(SCc2ccccc2)cn1) `ZINC000677168516.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000677168516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000677168516/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000677168516 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(SCc2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 5, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 6, 22, 44, 46, 46, 44, 46, 46, 6, 6, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 4, 6, 6, 44, 44, 46, 46, 46, 46, 46, 6] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 176 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000677168516 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000677168516 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000677168516/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000677168516/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000677168516 Building ZINC000677168516 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000677168516' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000677168516 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000677168516 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000677168516/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000677168516 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 686) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/686: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(SCc2ccccc2)cn1) `ZINC000677168516.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000677168516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000677168516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000677168516 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(SCc2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 5, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 20, 43, 45, 45, 45, 45, 45, 5, 5, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 3, 5, 5, 43, 43, 45, 45, 45, 45, 45, 5] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 160 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000677168516 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000677168516/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000677168516 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 687) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/687: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(SCc2ccccc2)cn1) `ZINC000677168516.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000677168516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000677168516/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000677168516 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(SCc2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 5, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 6, 22, 44, 46, 46, 44, 46, 46, 6, 6, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 4, 6, 6, 44, 44, 46, 46, 46, 46, 46, 6] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 176 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000677168516 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000677168516 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000677168516/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000677168516/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000677168516 Building ZINC000678997115 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000678997115' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000678997115 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000678997115 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000678997115/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000678997115 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 688) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/688 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/688' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(Cc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000678997115.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000678997115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000678997115/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000678997115 none CCN(Cc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 8, 8, 8, 8, 8, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 15, 15, 2, 15, 15, 15, 15, 15, 15, 2, 2, 4, 4, 4, 4, 4, 7, 7, 8, 8, 8, 8, 8, 2, 2, 2, 15, 15, 2, 15, 2, 2, 2] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 69 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000678997115 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000678997115/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000678997115 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 689) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/689 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/689' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(Cc1ccccc1)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000678997115.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000678997115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000678997115/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000678997115 none CCN(Cc1ccccc1)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 8, 8, 7, 8, 8, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 15, 15, 2, 15, 15, 15, 15, 15, 15, 2, 2, 4, 4, 4, 4, 4, 7, 7, 8, 8, 8, 8, 8, 2, 2, 2, 15, 15, 2, 15, 2, 2, 2] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 74 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000678997115 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000678997115 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000678997115/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000678997115/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000678997115 Building ZINC000678997115 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000678997115' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000678997115 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000678997115 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000678997115/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000678997115 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 688) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/688: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(Cc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000678997115.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000678997115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000678997115/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000678997115 none CCN(Cc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 8, 8, 8, 8, 8, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 15, 15, 2, 15, 15, 15, 15, 15, 15, 2, 2, 4, 4, 4, 4, 4, 7, 7, 8, 8, 8, 8, 8, 2, 2, 2, 15, 15, 2, 15, 2, 2, 2] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 69 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000678997115 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000678997115/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000678997115 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 689) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/689: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(Cc1ccccc1)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000678997115.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000678997115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000678997115/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000678997115 none CCN(Cc1ccccc1)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 8, 8, 7, 8, 8, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 15, 15, 2, 15, 15, 15, 15, 15, 15, 2, 2, 4, 4, 4, 4, 4, 7, 7, 8, 8, 8, 8, 8, 2, 2, 2, 15, 15, 2, 15, 2, 2, 2] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 74 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000678997115 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000678997115 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000678997115/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000678997115/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000678997115 Building ZINC000679003923 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679003923' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679003923 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000679003923 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679003923/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679003923 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 690) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/690 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/690' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccsc1CN(C)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000679003923.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000679003923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679003923/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000679003923 none Cc1ccsc1CN(C)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', '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, 14, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 8, 4, 2, 4, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 10, 10, 10, 10, 10, 8, 8, 4, 4, 4, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 58 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679003923 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679003923/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679003923 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 691) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/691 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/691' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccsc1CN(C)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000679003923.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000679003923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679003923/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000679003923 none Cc1ccsc1CN(C)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', '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, 14, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 8, 4, 2, 4, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 10, 10, 10, 10, 10, 8, 8, 4, 4, 4, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 58 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679003923 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000679003923 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679003923/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679003923/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679003923 Building ZINC000679003923 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679003923' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679003923 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000679003923 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679003923/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679003923 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 690) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/690: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccsc1CN(C)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000679003923.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000679003923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679003923/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000679003923 none Cc1ccsc1CN(C)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', '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, 14, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 8, 4, 2, 4, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 10, 10, 10, 10, 10, 8, 8, 4, 4, 4, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 58 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679003923 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679003923/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679003923 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 691) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/691: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccsc1CN(C)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000679003923.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000679003923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679003923/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000679003923 none Cc1ccsc1CN(C)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', '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, 14, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 8, 4, 2, 4, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 10, 10, 10, 10, 10, 8, 8, 4, 4, 4, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 58 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679003923 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000679003923 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679003923/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679003923/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679003923 Building ZINC000679005291 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679005291' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679005291 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000679005291 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679005291/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679005291 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 692) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/692 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/692' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c2ccccc2)cc1) `ZINC000679005291.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000679005291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679005291/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000679005291 none COc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 4, 4, 18, 18, 4, 2, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4, 10, 10, 4, 10, 10, 18, 18, 18, 18, 18, 18, 18, 2, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4, 10, 10, 4, 10, 10, 18, 18] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 120 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679005291 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679005291/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679005291 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 693) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/693 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/693' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c2ccccc2)cc1) `ZINC000679005291.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000679005291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679005291/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000679005291 none COc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 4, 23, 23, 4, 2, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4, 8, 8, 4, 8, 8, 23, 23, 23, 23, 23, 23, 23, 2, 4, 4, 4, 8, 8, 8, 8, 8, 4, 4, 4, 8, 8, 4, 8, 8, 23, 23] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 136 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679005291 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000679005291 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679005291/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679005291/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679005291 Building ZINC000679005291 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679005291' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679005291 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000679005291 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679005291/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679005291 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 692) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/692: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c2ccccc2)cc1) `ZINC000679005291.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000679005291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679005291/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000679005291 none COc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 4, 4, 18, 18, 4, 2, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4, 10, 10, 4, 10, 10, 18, 18, 18, 18, 18, 18, 18, 2, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4, 10, 10, 4, 10, 10, 18, 18] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 120 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679005291 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679005291/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679005291 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 693) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/693: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c2ccccc2)cc1) `ZINC000679005291.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000679005291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679005291/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000679005291 none COc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 4, 23, 23, 4, 2, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4, 8, 8, 4, 8, 8, 23, 23, 23, 23, 23, 23, 23, 2, 4, 4, 4, 8, 8, 8, 8, 8, 4, 4, 4, 8, 8, 4, 8, 8, 23, 23] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 136 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679005291 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000679005291 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679005291/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679005291/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679005291 Building ZINC000679005292 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679005292' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679005292 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000679005292 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679005292/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679005292 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 694) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/694 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/694' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c2ccccc2)cc1) `ZINC000679005292.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000679005292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679005292/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000679005292 none COc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 22, 22, 4, 2, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4, 8, 8, 4, 8, 8, 22, 22, 22, 22, 22, 22, 22, 2, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4, 8, 8, 4, 8, 8, 22, 22] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 125 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679005292 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679005292/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679005292 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 695) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/695 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/695' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c2ccccc2)cc1) `ZINC000679005292.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000679005292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679005292/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000679005292 none COc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 4, 2, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 9, 9, 4, 9, 9, 4, 4, 4, 10, 10, 4, 10, 10, 18, 18, 18, 18, 18, 18, 18, 2, 4, 4, 4, 9, 9, 8, 9, 9, 4, 4, 4, 10, 10, 4, 10, 10, 18, 18] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 93 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679005292 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000679005292 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679005292/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679005292/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679005292 Building ZINC000679005292 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679005292' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679005292 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000679005292 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679005292/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679005292 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 694) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/694: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c2ccccc2)cc1) `ZINC000679005292.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000679005292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679005292/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000679005292 none COc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 22, 22, 4, 2, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4, 8, 8, 4, 8, 8, 22, 22, 22, 22, 22, 22, 22, 2, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4, 8, 8, 4, 8, 8, 22, 22] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 125 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679005292 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679005292/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679005292 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 695) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/695: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c2ccccc2)cc1) `ZINC000679005292.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000679005292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679005292/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000679005292 none COc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 4, 2, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 9, 9, 4, 9, 9, 4, 4, 4, 10, 10, 4, 10, 10, 18, 18, 18, 18, 18, 18, 18, 2, 4, 4, 4, 9, 9, 8, 9, 9, 4, 4, 4, 10, 10, 4, 10, 10, 18, 18] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 93 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679005292 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000679005292 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679005292/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679005292/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000679005292 Building ZINC000680619456 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680619456' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680619456 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000680619456 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680619456/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680619456 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 696) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/696 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/696' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(NC(=O)C3CC3)cc2C(F)(F)F)cc1Cl) `ZINC000680619456.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000680619456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680619456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000680619456 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(NC(=O)C3CC3)cc2C(F)(F)F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 5, 15, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 2, 5, 5, 1, 1, 1, 1, 2, 2, 2, 5, 5, 4, 5, 11, 11, 11, 23, 23, 5, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 5, 5, 2, 5, 5, 11, 23, 23, 23, 23, 23, 5, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680619456 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680619456/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680619456 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 697) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/697 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/697' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(NC(=O)C3CC3)cc2C(F)(F)F)cc1Cl) `ZINC000680619456.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000680619456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680619456/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000680619456 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(NC(=O)C3CC3)cc2C(F)(F)F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 5, 15, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 5, 5, 2, 2, 10, 10, 10, 20, 20, 5, 5, 5, 5, 5, 5, 4, 4, 4, 10, 10, 10, 4, 4, 2, 5, 5, 10, 20, 20, 20, 20, 20, 5, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680619456 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000680619456 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680619456/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680619456/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680619456 Building ZINC000680619456 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680619456' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680619456 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000680619456 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680619456/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680619456 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 696) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/696: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(NC(=O)C3CC3)cc2C(F)(F)F)cc1Cl) `ZINC000680619456.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000680619456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680619456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000680619456 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(NC(=O)C3CC3)cc2C(F)(F)F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 5, 15, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 2, 5, 5, 1, 1, 1, 1, 2, 2, 2, 5, 5, 4, 5, 11, 11, 11, 23, 23, 5, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 5, 5, 2, 5, 5, 11, 23, 23, 23, 23, 23, 5, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680619456 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680619456/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680619456 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 697) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/697: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(NC(=O)C3CC3)cc2C(F)(F)F)cc1Cl) `ZINC000680619456.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000680619456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680619456/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000680619456 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(NC(=O)C3CC3)cc2C(F)(F)F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 5, 15, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 5, 5, 2, 2, 10, 10, 10, 20, 20, 5, 5, 5, 5, 5, 5, 4, 4, 4, 10, 10, 10, 4, 4, 2, 5, 5, 10, 20, 20, 20, 20, 20, 5, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680619456 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000680619456 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680619456/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680619456/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680619456 Building ZINC000680621004 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621004' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621004 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000680621004 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621004/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621004 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 698) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/698 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/698' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC2C[C@H](C(F)(F)F)C[C@@H](C(F)(F)F)C2)cc1Cl) `ZINC000680621004.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000680621004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621004/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000680621004 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC2C[C@H](C(F)(F)F)C[C@@H](C(F)(F)F)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 7, 5, 15, 15, 15, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 2, 2, 4, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 6, 6, 12, 12, 12, 6, 6, 2, 20, 20, 20, 20, 20, 20, 20, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621004 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621004/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621004 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 699) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/699 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/699' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC2C[C@H](C(F)(F)F)C[C@@H](C(F)(F)F)C2)cc1Cl) `ZINC000680621004.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000680621004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621004/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000680621004 none COc1ccc([C@]([O-])([SiH3])C(=O)NC2C[C@H](C(F)(F)F)C[C@@H](C(F)(F)F)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 7, 5, 15, 15, 15, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 2, 6, 6, 1, 1, 1, 1, 2, 2, 5, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 6, 6, 10, 10, 10, 6, 6, 2, 19, 19, 19, 19, 19, 19, 19, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621004 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000680621004 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621004/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621004/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621004 Building ZINC000680621004 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621004' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621004 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000680621004 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621004/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621004 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 698) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/698: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC2C[C@H](C(F)(F)F)C[C@@H](C(F)(F)F)C2)cc1Cl) `ZINC000680621004.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000680621004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621004/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000680621004 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC2C[C@H](C(F)(F)F)C[C@@H](C(F)(F)F)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 7, 5, 15, 15, 15, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 2, 2, 4, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 6, 6, 12, 12, 12, 6, 6, 2, 20, 20, 20, 20, 20, 20, 20, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621004 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621004/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621004 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 699) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/699: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC2C[C@H](C(F)(F)F)C[C@@H](C(F)(F)F)C2)cc1Cl) `ZINC000680621004.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000680621004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621004/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000680621004 none COc1ccc([C@]([O-])([SiH3])C(=O)NC2C[C@H](C(F)(F)F)C[C@@H](C(F)(F)F)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 7, 5, 15, 15, 15, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 2, 6, 6, 1, 1, 1, 1, 2, 2, 5, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 6, 6, 10, 10, 10, 6, 6, 2, 19, 19, 19, 19, 19, 19, 19, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621004 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000680621004 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621004/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621004/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621004 Building ZINC000680621005 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621005' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621005 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000680621005 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621005/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621005 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 700) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/700 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/700' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2C[C@H](C(F)(F)F)C[C@H](C(F)(F)F)C2)cc1Cl) `ZINC000680621005.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000680621005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621005/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000680621005 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2C[C@H](C(F)(F)F)C[C@H](C(F)(F)F)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 15, 15, 15, 5, 5, 7, 5, 15, 15, 15, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 2, 10, 10, 1, 1, 1, 1, 4, 4, 4, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 10, 10, 10, 20, 20, 20, 10, 10, 4, 15, 15, 15, 15, 15, 15, 10] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621005 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621005/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621005 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 701) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/701 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/701' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2C[C@H](C(F)(F)F)C[C@H](C(F)(F)F)C2)cc1Cl) `ZINC000680621005.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000680621005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621005/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000680621005 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2C[C@H](C(F)(F)F)C[C@H](C(F)(F)F)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 15, 15, 15, 5, 5, 7, 5, 15, 15, 15, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 3, 10, 10, 1, 1, 1, 1, 4, 4, 4, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 10, 10, 10, 20, 20, 20, 10, 10, 4, 15, 15, 15, 15, 15, 15, 10] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621005 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000680621005 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621005/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621005/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621005 Building ZINC000680621005 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621005' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621005 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000680621005 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621005/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621005 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 700) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/700: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2C[C@H](C(F)(F)F)C[C@H](C(F)(F)F)C2)cc1Cl) `ZINC000680621005.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000680621005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621005/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000680621005 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2C[C@H](C(F)(F)F)C[C@H](C(F)(F)F)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 15, 15, 15, 5, 5, 7, 5, 15, 15, 15, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 2, 10, 10, 1, 1, 1, 1, 4, 4, 4, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 10, 10, 10, 20, 20, 20, 10, 10, 4, 15, 15, 15, 15, 15, 15, 10] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621005 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621005/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621005 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 701) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/701: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2C[C@H](C(F)(F)F)C[C@H](C(F)(F)F)C2)cc1Cl) `ZINC000680621005.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000680621005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621005/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000680621005 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2C[C@H](C(F)(F)F)C[C@H](C(F)(F)F)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 15, 15, 15, 5, 5, 7, 5, 15, 15, 15, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 3, 10, 10, 1, 1, 1, 1, 4, 4, 4, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 10, 10, 10, 20, 20, 20, 10, 10, 4, 15, 15, 15, 15, 15, 15, 10] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621005 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000680621005 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621005/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621005/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621005 Building ZINC000680621006 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621006' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621006 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000680621006 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621006/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621006 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 702) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/702 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/702' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC2C[C@@H](C(F)(F)F)C[C@H](C(F)(F)F)C2)cc1Cl) `ZINC000680621006.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000680621006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000680621006 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC2C[C@@H](C(F)(F)F)C[C@H](C(F)(F)F)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 7, 5, 15, 15, 15, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 2, 2, 5, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 6, 6, 11, 11, 11, 6, 6, 2, 20, 20, 20, 20, 20, 20, 20, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621006 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621006/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621006 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 703) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/703 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/703' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC2C[C@@H](C(F)(F)F)C[C@H](C(F)(F)F)C2)cc1Cl) `ZINC000680621006.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000680621006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621006/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000680621006 none COc1ccc([C@]([O-])([SiH3])C(=O)NC2C[C@@H](C(F)(F)F)C[C@H](C(F)(F)F)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 7, 5, 15, 15, 15, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 2, 2, 5, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 6, 6, 12, 12, 12, 6, 6, 2, 20, 20, 20, 20, 20, 20, 20, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621006 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000680621006 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621006/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621006/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621006 Building ZINC000680621006 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621006' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621006 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000680621006 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621006/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621006 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 702) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/702: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC2C[C@@H](C(F)(F)F)C[C@H](C(F)(F)F)C2)cc1Cl) `ZINC000680621006.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000680621006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000680621006 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC2C[C@@H](C(F)(F)F)C[C@H](C(F)(F)F)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 7, 5, 15, 15, 15, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 2, 2, 5, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 6, 6, 11, 11, 11, 6, 6, 2, 20, 20, 20, 20, 20, 20, 20, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621006 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621006/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621006 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 703) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/703: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC2C[C@@H](C(F)(F)F)C[C@H](C(F)(F)F)C2)cc1Cl) `ZINC000680621006.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000680621006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621006/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000680621006 none COc1ccc([C@]([O-])([SiH3])C(=O)NC2C[C@@H](C(F)(F)F)C[C@H](C(F)(F)F)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 7, 5, 15, 15, 15, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 2, 2, 5, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 6, 6, 12, 12, 12, 6, 6, 2, 20, 20, 20, 20, 20, 20, 20, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621006 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000680621006 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621006/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621006/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680621006 Building ZINC000680650553 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680650553' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680650553 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000680650553 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680650553/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680650553 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 704) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/704 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/704' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1) `ZINC000680650553.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000680650553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680650553/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000680650553 none CCOc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 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, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 10, 7, 6, 7, 7, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 16, 16, 3, 16, 16, 16, 16, 16, 16, 3, 3, 7, 7, 12, 12, 12, 12, 12, 7, 7, 2, 3, 3, 3, 16, 16, 6, 16, 3, 3, 3, 7, 7] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680650553 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680650553/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680650553 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 705) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/705 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/705' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1) `ZINC000680650553.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000680650553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680650553/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000680650553 none CCOc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 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, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 7, 7, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 16, 16, 3, 16, 16, 16, 16, 16, 16, 3, 3, 7, 7, 11, 11, 11, 11, 11, 7, 7, 2, 3, 3, 3, 16, 16, 3, 16, 3, 3, 3, 7, 7] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680650553 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000680650553 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680650553/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680650553/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680650553 Building ZINC000680650553 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680650553' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680650553 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000680650553 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680650553/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680650553 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 704) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/704: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1) `ZINC000680650553.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000680650553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680650553/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000680650553 none CCOc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 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, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 10, 7, 6, 7, 7, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 16, 16, 3, 16, 16, 16, 16, 16, 16, 3, 3, 7, 7, 12, 12, 12, 12, 12, 7, 7, 2, 3, 3, 3, 16, 16, 6, 16, 3, 3, 3, 7, 7] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680650553 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680650553/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680650553 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 705) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/705: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1) `ZINC000680650553.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000680650553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680650553/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000680650553 none CCOc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 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, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 7, 7, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 16, 16, 3, 16, 16, 16, 16, 16, 16, 3, 3, 7, 7, 11, 11, 11, 11, 11, 7, 7, 2, 3, 3, 3, 16, 16, 3, 16, 3, 3, 3, 7, 7] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680650553 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000680650553 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680650553/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680650553/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680650553 Building ZINC000680672226 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680672226' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680672226 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000680672226 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680672226/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680672226 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 706) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/706 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/706' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C)cc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000680672226.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000680672226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680672226/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000680672226 none COc1ccc(C)cc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', '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, 12, 1, 1, 1, 1, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 6, 6, 5, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 13, 13, 2, 13, 13, 13, 13, 13, 13, 2, 2, 11, 11, 11, 6, 6, 6, 6, 6, 6, 2, 2, 2, 2, 13, 13, 2, 13, 2, 2, 2] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 55 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680672226 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680672226/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680672226 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 707) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/707 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/707' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C)cc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000680672226.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000680672226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680672226/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000680672226 none COc1ccc(C)cc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', '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, 12, 1, 1, 1, 1, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 6, 6, 5, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 16, 16, 3, 16, 16, 16, 16, 16, 16, 3, 3, 10, 10, 10, 6, 6, 6, 6, 6, 6, 2, 3, 3, 3, 16, 16, 4, 16, 3, 3, 3] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 63 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680672226 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000680672226 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680672226/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680672226/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680672226 Building ZINC000680672226 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680672226' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680672226 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000680672226 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680672226/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680672226 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 706) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/706: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C)cc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000680672226.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000680672226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680672226/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000680672226 none COc1ccc(C)cc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', '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, 12, 1, 1, 1, 1, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 6, 6, 5, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 13, 13, 2, 13, 13, 13, 13, 13, 13, 2, 2, 11, 11, 11, 6, 6, 6, 6, 6, 6, 2, 2, 2, 2, 13, 13, 2, 13, 2, 2, 2] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 55 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680672226 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680672226/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680672226 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 707) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/707: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C)cc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000680672226.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000680672226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680672226/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000680672226 none COc1ccc(C)cc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', '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, 12, 1, 1, 1, 1, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 6, 6, 5, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 16, 16, 3, 16, 16, 16, 16, 16, 16, 3, 3, 10, 10, 10, 6, 6, 6, 6, 6, 6, 2, 3, 3, 3, 16, 16, 4, 16, 3, 3, 3] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 63 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680672226 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000680672226 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680672226/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680672226/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000680672226 Building ZINC000682735435 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000682735435' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000682735435 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000682735435 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000682735435/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000682735435 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 708) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/708 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/708' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000682735435.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000682735435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000682735435/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000682735435 none CCOc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 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, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 4, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 14, 14, 14, 14, 14, 5, 5, 5, 5, 2, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000682735435 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000682735435/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000682735435 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 709) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/709 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/709' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccccc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000682735435.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000682735435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000682735435/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000682735435 none CCOc1ccccc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 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, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 4, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 14, 14, 14, 14, 14, 5, 5, 5, 5, 2, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000682735435 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000682735435 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000682735435/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000682735435/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000682735435 Building ZINC000682735435 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000682735435' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000682735435 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000682735435 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000682735435/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000682735435 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 708) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/708: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000682735435.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000682735435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000682735435/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000682735435 none CCOc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 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, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 4, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 14, 14, 14, 14, 14, 5, 5, 5, 5, 2, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000682735435 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000682735435/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000682735435 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 709) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/709: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccccc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000682735435.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000682735435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000682735435/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000682735435 none CCOc1ccccc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 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, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 4, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 14, 14, 14, 14, 14, 5, 5, 5, 5, 2, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000682735435 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000682735435 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000682735435/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000682735435/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000682735435 Building ZINC001276389376 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276389376' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276389376 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001276389376 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276389376/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276389376 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 710) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/710 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/710' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c(F)c1) `ZINC001276389376.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001276389376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276389376/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001276389376 none CCOc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'F', '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, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 12, 4, 2, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 4, 4, 4, 15, 15, 15, 15, 15, 4, 4, 2, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2, 4] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276389376 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276389376/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276389376 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 711) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/711 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/711' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c(F)c1) `ZINC001276389376.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001276389376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276389376/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001276389376 none CCOc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'F', '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, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 2, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 11, 11, 2, 11, 11, 11, 11, 11, 11, 2, 2, 4, 4, 4, 13, 13, 13, 13, 13, 4, 4, 2, 2, 2, 2, 11, 11, 4, 11, 2, 2, 2, 4] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276389376 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001276389376 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276389376/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276389376/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276389376 Building ZINC001276389376 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276389376' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276389376 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001276389376 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276389376/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276389376 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 710) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/710: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c(F)c1) `ZINC001276389376.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001276389376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276389376/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001276389376 none CCOc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'F', '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, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 12, 4, 2, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 4, 4, 4, 15, 15, 15, 15, 15, 4, 4, 2, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2, 4] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276389376 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276389376/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276389376 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 711) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/711: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c(F)c1) `ZINC001276389376.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001276389376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276389376/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001276389376 none CCOc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'F', '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, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 2, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 11, 11, 2, 11, 11, 11, 11, 11, 11, 2, 2, 4, 4, 4, 13, 13, 13, 13, 13, 4, 4, 2, 2, 2, 2, 11, 11, 4, 11, 2, 2, 2, 4] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276389376 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001276389376 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276389376/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276389376/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276389376 Building ZINC000750227243 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000750227243' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000750227243 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000750227243 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000750227243/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000750227243 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 712) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/712 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/712' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)c1cccnc1) `ZINC000750227243.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000750227243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000750227243/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000750227243 none CCCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 2, 6, 6, 6, 6, 6, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 6, 6, 6, 6] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000750227243 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000750227243/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000750227243 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 713) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/713 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/713' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)c1cccnc1) `ZINC000750227243.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000750227243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000750227243/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000750227243 none CCCN(C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 2, 6, 6, 6, 6, 6, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 6, 6, 6, 6] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000750227243 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000750227243 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000750227243/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000750227243/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000750227243 Building ZINC000750227243 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000750227243' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000750227243 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000750227243 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000750227243/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000750227243 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 712) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/712: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)c1cccnc1) `ZINC000750227243.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000750227243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000750227243/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000750227243 none CCCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 2, 6, 6, 6, 6, 6, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 6, 6, 6, 6] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000750227243 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000750227243/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000750227243 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 713) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/713: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)c1cccnc1) `ZINC000750227243.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000750227243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000750227243/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000750227243 none CCCN(C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 2, 6, 6, 6, 6, 6, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 6, 6, 6, 6] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000750227243 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000750227243 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000750227243/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000750227243/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000750227243 Building ZINC000752116369 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116369' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116369 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000752116369 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116369/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116369 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 714) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/714 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/714' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@H]1C[C@@H](O)c1ccccc1) `ZINC000752116369.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000752116369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116369/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000752116369 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@H]1C[C@@H](O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 6, 11, 11, 3, 3, 1, 1, 1, 1, 9, 10, 12, 12, 12, 12, 12, 12, 12, 12, 22, 36, 36, 36, 44, 44, 36, 44, 44, 3, 3, 3, 11, 11, 11, 11, 11, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 22, 22, 108, 44, 44, 36, 44, 44] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 343 number of broken/clashed sets: 55 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116369 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116369/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116369 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 715) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/715 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/715' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCCC[C@H]1C[C@@H](O)c1ccccc1) `ZINC000752116369.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000752116369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116369/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000752116369 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCCC[C@H]1C[C@@H](O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 6, 8, 8, 3, 3, 1, 1, 1, 2, 9, 9, 10, 10, 10, 10, 10, 10, 10, 10, 21, 35, 35, 35, 40, 40, 35, 40, 40, 3, 3, 3, 8, 8, 6, 8, 8, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 21, 21, 105, 40, 40, 35, 40, 40] 150 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 285 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116369 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000752116369 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116369/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116369/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116369 Building ZINC000752116369 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116369' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116369 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000752116369 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116369/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116369 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 714) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/714: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@H]1C[C@@H](O)c1ccccc1) `ZINC000752116369.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000752116369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116369/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000752116369 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@H]1C[C@@H](O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 6, 11, 11, 3, 3, 1, 1, 1, 1, 9, 10, 12, 12, 12, 12, 12, 12, 12, 12, 22, 36, 36, 36, 44, 44, 36, 44, 44, 3, 3, 3, 11, 11, 11, 11, 11, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 22, 22, 108, 44, 44, 36, 44, 44] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 343 number of broken/clashed sets: 55 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116369 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116369/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116369 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 715) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/715: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCCC[C@H]1C[C@@H](O)c1ccccc1) `ZINC000752116369.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000752116369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116369/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000752116369 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCCC[C@H]1C[C@@H](O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 6, 8, 8, 3, 3, 1, 1, 1, 2, 9, 9, 10, 10, 10, 10, 10, 10, 10, 10, 21, 35, 35, 35, 40, 40, 35, 40, 40, 3, 3, 3, 8, 8, 6, 8, 8, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 21, 21, 105, 40, 40, 35, 40, 40] 150 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 285 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116369 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000752116369 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116369/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116369/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116369 Building ZINC000752116372 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116372' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116372 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000752116372 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116372/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116372 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 716) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/716 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/716' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@@H]1C[C@@H](O)c1ccccc1) `ZINC000752116372.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000752116372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116372/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000752116372 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@@H]1C[C@@H](O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 9, 11, 11, 11, 11, 11, 11, 11, 11, 11, 23, 35, 35, 35, 41, 41, 35, 41, 41, 3, 3, 3, 8, 8, 5, 8, 8, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 23, 23, 105, 41, 41, 35, 41, 41] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 305 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116372 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116372/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116372 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 717) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/717 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/717' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCCC[C@@H]1C[C@@H](O)c1ccccc1) `ZINC000752116372.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000752116372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116372/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000752116372 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCCC[C@@H]1C[C@@H](O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 6, 8, 8, 3, 3, 1, 1, 1, 1, 8, 10, 11, 11, 11, 11, 11, 11, 11, 11, 24, 36, 36, 36, 43, 43, 43, 43, 43, 3, 3, 3, 8, 8, 6, 8, 8, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 24, 24, 108, 43, 43, 43, 43, 43] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 283 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116372 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000752116372 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116372/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116372/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116372 Building ZINC000752116372 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116372' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116372 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000752116372 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116372/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116372 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 716) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/716: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@@H]1C[C@@H](O)c1ccccc1) `ZINC000752116372.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000752116372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116372/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000752116372 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@@H]1C[C@@H](O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 9, 11, 11, 11, 11, 11, 11, 11, 11, 11, 23, 35, 35, 35, 41, 41, 35, 41, 41, 3, 3, 3, 8, 8, 5, 8, 8, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 23, 23, 105, 41, 41, 35, 41, 41] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 305 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116372 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116372/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116372 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 717) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/717: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCCC[C@@H]1C[C@@H](O)c1ccccc1) `ZINC000752116372.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000752116372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116372/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000752116372 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCCC[C@@H]1C[C@@H](O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 6, 8, 8, 3, 3, 1, 1, 1, 1, 8, 10, 11, 11, 11, 11, 11, 11, 11, 11, 24, 36, 36, 36, 43, 43, 43, 43, 43, 3, 3, 3, 8, 8, 6, 8, 8, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 24, 24, 108, 43, 43, 43, 43, 43] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 283 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116372 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000752116372 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116372/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116372/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116372 Building ZINC000752116375 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116375' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116375 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000752116375 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116375/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116375 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 718) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/718 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/718' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@@H]1C[C@H](O)c1ccccc1) `ZINC000752116375.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000752116375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116375/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000752116375 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@@H]1C[C@H](O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 10, 10, 4, 10, 10, 4, 4, 1, 1, 1, 1, 7, 9, 10, 10, 10, 10, 10, 10, 10, 10, 18, 33, 33, 33, 38, 38, 34, 38, 38, 4, 4, 4, 10, 10, 5, 10, 10, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 18, 18, 99, 38, 38, 34, 38, 38] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 272 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116375 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116375/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116375 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 719) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/719 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/719' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCCC[C@@H]1C[C@H](O)c1ccccc1) `ZINC000752116375.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000752116375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116375/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000752116375 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCCC[C@@H]1C[C@H](O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 6, 8, 8, 3, 3, 1, 1, 1, 1, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 18, 33, 33, 33, 45, 45, 33, 45, 45, 3, 3, 3, 8, 8, 6, 8, 8, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 18, 18, 99, 45, 45, 33, 45, 45] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 310 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116375 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000752116375 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116375/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116375/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116375 Building ZINC000752116375 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116375' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116375 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000752116375 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116375/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116375 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 718) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/718: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@@H]1C[C@H](O)c1ccccc1) `ZINC000752116375.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000752116375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116375/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000752116375 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@@H]1C[C@H](O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 10, 10, 4, 10, 10, 4, 4, 1, 1, 1, 1, 7, 9, 10, 10, 10, 10, 10, 10, 10, 10, 18, 33, 33, 33, 38, 38, 34, 38, 38, 4, 4, 4, 10, 10, 5, 10, 10, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 18, 18, 99, 38, 38, 34, 38, 38] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 272 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116375 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116375/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116375 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 719) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/719: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCCC[C@@H]1C[C@H](O)c1ccccc1) `ZINC000752116375.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000752116375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116375/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000752116375 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCCC[C@@H]1C[C@H](O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 6, 8, 8, 3, 3, 1, 1, 1, 1, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 18, 33, 33, 33, 45, 45, 33, 45, 45, 3, 3, 3, 8, 8, 6, 8, 8, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 18, 18, 99, 45, 45, 33, 45, 45] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 310 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116375 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000752116375 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116375/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116375/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116375 Building ZINC000752116378 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116378' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116378 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000752116378 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116378/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116378 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 720) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/720 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/720' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@H]1C[C@H](O)c1ccccc1) `ZINC000752116378.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000752116378.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116378/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000752116378 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@H]1C[C@H](O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 6, 9, 9, 3, 3, 1, 1, 1, 2, 8, 8, 10, 10, 10, 10, 10, 10, 10, 10, 22, 34, 34, 34, 43, 43, 35, 43, 43, 3, 3, 3, 9, 9, 9, 9, 9, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 22, 22, 102, 43, 43, 34, 43, 43] 150 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 316 number of broken/clashed sets: 66 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116378 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116378/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116378 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 721) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/721 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/721' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCCC[C@H]1C[C@H](O)c1ccccc1) `ZINC000752116378.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000752116378.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116378/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000752116378 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCCC[C@H]1C[C@H](O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 6, 8, 8, 3, 3, 1, 1, 1, 2, 9, 9, 10, 10, 10, 10, 10, 10, 10, 10, 24, 39, 39, 39, 43, 43, 39, 43, 43, 3, 3, 3, 8, 8, 6, 8, 8, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 24, 24, 117, 43, 43, 39, 43, 43] 150 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 310 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116378 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000752116378 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116378/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116378/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116378 Building ZINC000752116378 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116378' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116378 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000752116378 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116378/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116378 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 720) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/720: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@H]1C[C@H](O)c1ccccc1) `ZINC000752116378.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000752116378.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116378/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000752116378 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@H]1C[C@H](O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 6, 9, 9, 3, 3, 1, 1, 1, 2, 8, 8, 10, 10, 10, 10, 10, 10, 10, 10, 22, 34, 34, 34, 43, 43, 35, 43, 43, 3, 3, 3, 9, 9, 9, 9, 9, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 22, 22, 102, 43, 43, 34, 43, 43] 150 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 316 number of broken/clashed sets: 66 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116378 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116378/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116378 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 721) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/721: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCCC[C@H]1C[C@H](O)c1ccccc1) `ZINC000752116378.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000752116378.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116378/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000752116378 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCCC[C@H]1C[C@H](O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 6, 8, 8, 3, 3, 1, 1, 1, 2, 9, 9, 10, 10, 10, 10, 10, 10, 10, 10, 24, 39, 39, 39, 43, 43, 39, 43, 43, 3, 3, 3, 8, 8, 6, 8, 8, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 24, 24, 117, 43, 43, 39, 43, 43] 150 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 310 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116378 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000752116378 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116378/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116378/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752116378 Building ZINC000752374823 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752374823' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752374823 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000752374823 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752374823/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752374823 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 722) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/722 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/722' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nc2c(cc(OC(F)(F)F)cc2Br)s1) `ZINC000752374823.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000752374823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752374823/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000752374823 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nc2c(cc(OC(F)(F)F)cc2Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 17, 14, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 11, 11, 46, 50, 50, 50, 11, 11, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 11, 11] 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]) total number of confs: 98 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752374823 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752374823/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752374823 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 723) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/723 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/723' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nc2c(cc(OC(F)(F)F)cc2Br)s1) `ZINC000752374823.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000752374823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752374823/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000752374823 none CC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nc2c(cc(OC(F)(F)F)cc2Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 17, 14, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 1, 1, 1, 7, 7, 7, 11, 11, 11, 11, 11, 11, 45, 50, 50, 50, 11, 11, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 11, 11] 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]) total number of confs: 106 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752374823 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000752374823 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752374823/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752374823/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752374823 Building ZINC000752374823 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752374823' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752374823 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000752374823 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752374823/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752374823 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 722) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/722: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nc2c(cc(OC(F)(F)F)cc2Br)s1) `ZINC000752374823.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000752374823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752374823/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000752374823 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nc2c(cc(OC(F)(F)F)cc2Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 17, 14, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 11, 11, 46, 50, 50, 50, 11, 11, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 11, 11] 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]) total number of confs: 98 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752374823 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752374823/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752374823 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 723) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/723: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nc2c(cc(OC(F)(F)F)cc2Br)s1) `ZINC000752374823.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000752374823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752374823/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000752374823 none CC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nc2c(cc(OC(F)(F)F)cc2Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 17, 14, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 1, 1, 1, 7, 7, 7, 11, 11, 11, 11, 11, 11, 45, 50, 50, 50, 11, 11, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 11, 11] 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]) total number of confs: 106 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752374823 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000752374823 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752374823/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752374823/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000752374823 Building ZINC000754642809 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000754642809' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000754642809 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000754642809 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000754642809/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000754642809 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 724) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/724 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/724' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cnc(Cl)c(C)c1) `ZINC000754642809.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000754642809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000754642809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000754642809 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cnc(Cl)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 16, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 14, 14, 3, 14, 14, 14, 14, 14, 14, 3, 3, 1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 14, 14, 3, 14, 3, 3, 3, 3, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 52 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000754642809 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000754642809/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000754642809 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 725) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/725 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/725' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cnc(Cl)c(C)c1) `ZINC000754642809.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000754642809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000754642809/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000754642809 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cnc(Cl)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 16, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 14, 14, 4, 14, 14, 14, 14, 14, 14, 4, 4, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 4, 4, 4, 14, 14, 4, 14, 4, 4, 4, 3, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 48 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000754642809 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000754642809 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000754642809/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000754642809/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000754642809 Building ZINC000754642809 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000754642809' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000754642809 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000754642809 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000754642809/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000754642809 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 724) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/724: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cnc(Cl)c(C)c1) `ZINC000754642809.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000754642809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000754642809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000754642809 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cnc(Cl)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 16, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 14, 14, 3, 14, 14, 14, 14, 14, 14, 3, 3, 1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 14, 14, 3, 14, 3, 3, 3, 3, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 52 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000754642809 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000754642809/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000754642809 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 725) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/725: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cnc(Cl)c(C)c1) `ZINC000754642809.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000754642809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000754642809/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000754642809 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cnc(Cl)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 16, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 14, 14, 4, 14, 14, 14, 14, 14, 14, 4, 4, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 4, 4, 4, 14, 14, 4, 14, 4, 4, 4, 3, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 48 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000754642809 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000754642809 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000754642809/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000754642809/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000754642809 Building ZINC000758077208 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758077208' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758077208 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000758077208 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758077208/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758077208 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 726) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/726 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/726' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(N2C(=O)c3ccccc3C2=O)c(Cl)c1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000758077208.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000758077208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758077208/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000758077208 none O=C(Nc1ccc(N2C(=O)c3ccccc3C2=O)c(Cl)c1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 16, 1, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 16, 16, 14, 16, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 16, 16, 16, 1, 1, 1, 8, 8, 8, 8, 8, 3, 16, 16, 29, 29, 29, 29, 16, 8, 8] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758077208 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758077208/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758077208 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 727) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/727 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/727' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(N2C(=O)c3ccccc3C2=O)c(Cl)c1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000758077208.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000758077208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758077208/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000758077208 none O=C(Nc1ccc(N2C(=O)c3ccccc3C2=O)c(Cl)c1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 16, 1, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 15, 15, 11, 15, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 15, 15, 15, 1, 1, 1, 9, 9, 9, 9, 9, 3, 15, 15, 28, 28, 28, 28, 15, 9, 9] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758077208 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000758077208 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758077208/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758077208/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758077208 Building ZINC000758077208 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758077208' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758077208 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000758077208 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758077208/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758077208 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 726) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/726: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(N2C(=O)c3ccccc3C2=O)c(Cl)c1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000758077208.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000758077208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758077208/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000758077208 none O=C(Nc1ccc(N2C(=O)c3ccccc3C2=O)c(Cl)c1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 16, 1, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 16, 16, 14, 16, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 16, 16, 16, 1, 1, 1, 8, 8, 8, 8, 8, 3, 16, 16, 29, 29, 29, 29, 16, 8, 8] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758077208 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758077208/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758077208 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 727) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/727: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(N2C(=O)c3ccccc3C2=O)c(Cl)c1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000758077208.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000758077208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758077208/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000758077208 none O=C(Nc1ccc(N2C(=O)c3ccccc3C2=O)c(Cl)c1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 16, 1, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 15, 15, 11, 15, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 15, 15, 15, 1, 1, 1, 9, 9, 9, 9, 9, 3, 15, 15, 28, 28, 28, 28, 15, 9, 9] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758077208 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000758077208 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758077208/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758077208/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758077208 Building ZINC000758160920 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758160920' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758160920 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000758160920 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758160920/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758160920 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 728) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/728 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/728' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)c1C(=O)NCCc1ccccc1) `ZINC000758160920.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000758160920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758160920/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000758160920 none Cc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)c1C(=O)NCCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 9, 10, 10, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 10, 10, 16, 16, 16, 33, 42, 42, 42, 42, 42, 42, 10, 10, 10, 10, 10, 10, 4, 6, 6, 16, 33, 33, 42, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 180 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758160920 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758160920/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758160920 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 729) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/729 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/729' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)c1C(=O)NCCc1ccccc1) `ZINC000758160920.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000758160920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758160920/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000758160920 none Cc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)c1C(=O)NCCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 9, 9, 15, 15, 15, 34, 42, 42, 42, 42, 42, 42, 9, 9, 9, 9, 9, 9, 4, 6, 6, 15, 34, 34, 42, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 177 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758160920 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000758160920 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758160920/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758160920/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758160920 Building ZINC000758160920 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758160920' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758160920 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000758160920 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758160920/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758160920 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 728) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/728: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)c1C(=O)NCCc1ccccc1) `ZINC000758160920.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000758160920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758160920/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000758160920 none Cc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)c1C(=O)NCCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 9, 10, 10, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 10, 10, 16, 16, 16, 33, 42, 42, 42, 42, 42, 42, 10, 10, 10, 10, 10, 10, 4, 6, 6, 16, 33, 33, 42, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 180 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758160920 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758160920/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758160920 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 729) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/729: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)c1C(=O)NCCc1ccccc1) `ZINC000758160920.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000758160920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758160920/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC000758160920 none Cc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)c1C(=O)NCCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 9, 9, 15, 15, 15, 34, 42, 42, 42, 42, 42, 42, 9, 9, 9, 9, 9, 9, 4, 6, 6, 15, 34, 34, 42, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 177 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758160920 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000758160920 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758160920/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758160920/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758160920 Building ZINC000758265487 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000758265487 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 730) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/730 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/730' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)cc2C(F)(F)F)CC1) `ZINC000758265487.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000758265487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000758265487 none CO[C@H]1CC[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)cc2C(F)(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 5, 15, 15, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 30, 29, 29, 29, 29, 7, 2, 11, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 29, 29, 33, 33, 33, 29, 29, 29, 29, 11, 11, 2, 6, 6, 11, 29, 29, 29, 29] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 731) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/731 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/731' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)cc2C(F)(F)F)CC1) `ZINC000758265487.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000758265487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000758265487 none CO[C@H]1CC[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)cc2C(F)(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 5, 15, 15, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 30, 29, 29, 29, 29, 8, 2, 11, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 29, 29, 33, 33, 33, 29, 29, 29, 29, 11, 11, 2, 6, 6, 11, 29, 29, 29, 29] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 732) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/732 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/732' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)cc2C(F)(F)F)CC1) `ZINC000758265487.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000758265487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000758265487 none CO[C@H]1CC[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)cc2C(F)(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 5, 15, 15, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 34, 34, 34, 34, 34, 17, 8, 11, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 34, 34, 37, 37, 37, 34, 34, 34, 34, 11, 11, 2, 6, 6, 11, 34, 34, 34, 34] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 733) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/733 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/733' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)cc2C(F)(F)F)CC1) `ZINC000758265487.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000758265487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000758265487 none CO[C@H]1CC[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)cc2C(F)(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 5, 15, 15, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 34, 34, 34, 34, 4, 2, 11, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 34, 34, 38, 38, 38, 34, 34, 34, 34, 11, 11, 2, 6, 6, 11, 34, 34, 34, 34] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000758265487 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487 Building ZINC000758265487 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000758265487 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 730) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/730: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)cc2C(F)(F)F)CC1) `ZINC000758265487.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000758265487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000758265487 none CO[C@H]1CC[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)cc2C(F)(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 5, 15, 15, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 30, 29, 29, 29, 29, 7, 2, 11, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 29, 29, 33, 33, 33, 29, 29, 29, 29, 11, 11, 2, 6, 6, 11, 29, 29, 29, 29] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 731) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/731: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)cc2C(F)(F)F)CC1) `ZINC000758265487.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000758265487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000758265487 none CO[C@H]1CC[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)cc2C(F)(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 5, 15, 15, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 30, 29, 29, 29, 29, 8, 2, 11, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 29, 29, 33, 33, 33, 29, 29, 29, 29, 11, 11, 2, 6, 6, 11, 29, 29, 29, 29] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 732) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/732: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)cc2C(F)(F)F)CC1) `ZINC000758265487.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000758265487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000758265487 none CO[C@H]1CC[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)cc2C(F)(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 5, 15, 15, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 34, 34, 34, 34, 34, 17, 8, 11, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 34, 34, 37, 37, 37, 34, 34, 34, 34, 11, 11, 2, 6, 6, 11, 34, 34, 34, 34] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 733) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/733: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)cc2C(F)(F)F)CC1) `ZINC000758265487.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000758265487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000758265487 none CO[C@H]1CC[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)cc2C(F)(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 5, 15, 15, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 34, 34, 34, 34, 4, 2, 11, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 34, 34, 38, 38, 38, 34, 34, 34, 34, 11, 11, 2, 6, 6, 11, 34, 34, 34, 34] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000758265487 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487 Building ZINC000758265487 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000758265487 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 730) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/730: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)cc2C(F)(F)F)CC1) `ZINC000758265487.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000758265487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000758265487 none CO[C@H]1CC[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)cc2C(F)(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 5, 15, 15, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 30, 29, 29, 29, 29, 7, 2, 11, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 29, 29, 33, 33, 33, 29, 29, 29, 29, 11, 11, 2, 6, 6, 11, 29, 29, 29, 29] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 731) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/731: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)cc2C(F)(F)F)CC1) `ZINC000758265487.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000758265487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000758265487 none CO[C@H]1CC[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)cc2C(F)(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 5, 15, 15, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 30, 29, 29, 29, 29, 8, 2, 11, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 29, 29, 33, 33, 33, 29, 29, 29, 29, 11, 11, 2, 6, 6, 11, 29, 29, 29, 29] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 732) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/732: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)cc2C(F)(F)F)CC1) `ZINC000758265487.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000758265487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000758265487 none CO[C@H]1CC[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)cc2C(F)(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 5, 15, 15, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 34, 34, 34, 34, 34, 17, 8, 11, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 34, 34, 37, 37, 37, 34, 34, 34, 34, 11, 11, 2, 6, 6, 11, 34, 34, 34, 34] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 733) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/733: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)cc2C(F)(F)F)CC1) `ZINC000758265487.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000758265487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000758265487 none CO[C@H]1CC[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)cc2C(F)(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 5, 15, 15, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 34, 34, 34, 34, 4, 2, 11, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 34, 34, 38, 38, 38, 34, 34, 34, 34, 11, 11, 2, 6, 6, 11, 34, 34, 34, 34] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000758265487 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487 Building ZINC000758265487 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000758265487 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 730) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/730: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)cc2C(F)(F)F)CC1) `ZINC000758265487.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000758265487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000758265487 none CO[C@H]1CC[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)cc2C(F)(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 5, 15, 15, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 30, 29, 29, 29, 29, 7, 2, 11, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 29, 29, 33, 33, 33, 29, 29, 29, 29, 11, 11, 2, 6, 6, 11, 29, 29, 29, 29] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 731) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/731: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)cc2C(F)(F)F)CC1) `ZINC000758265487.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000758265487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000758265487 none CO[C@H]1CC[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)cc2C(F)(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 5, 15, 15, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 30, 29, 29, 29, 29, 8, 2, 11, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 29, 29, 33, 33, 33, 29, 29, 29, 29, 11, 11, 2, 6, 6, 11, 29, 29, 29, 29] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 732) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/732: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)cc2C(F)(F)F)CC1) `ZINC000758265487.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000758265487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000758265487 none CO[C@H]1CC[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)cc2C(F)(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 5, 15, 15, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 34, 34, 34, 34, 34, 17, 8, 11, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 34, 34, 37, 37, 37, 34, 34, 34, 34, 11, 11, 2, 6, 6, 11, 34, 34, 34, 34] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 733) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/733: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)cc2C(F)(F)F)CC1) `ZINC000758265487.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000758265487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000758265487 none CO[C@H]1CC[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)cc2C(F)(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 5, 15, 15, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 34, 34, 34, 34, 4, 2, 11, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 34, 34, 38, 38, 38, 34, 34, 34, 34, 11, 11, 2, 6, 6, 11, 34, 34, 34, 34] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000758265487 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758265487 Building ZINC000758283416 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758283416' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758283416 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000758283416 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758283416/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758283416 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 734) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/734 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/734' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)c1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)sc2c1-c1ccccc1CCC2) `ZINC000758283416.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000758283416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758283416/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000758283416 none NC(=O)c1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)sc2c1-c1ccccc1CCC2 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 24, 29, 15, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 15, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 29, 29, 4, 8, 8, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 95 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758283416 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758283416/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758283416 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 735) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/735 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/735' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)c1c(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)sc2c1-c1ccccc1CCC2) `ZINC000758283416.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000758283416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758283416/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000758283416 none NC(=O)c1c(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)sc2c1-c1ccccc1CCC2 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 24, 29, 15, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 15, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 29, 29, 4, 8, 8, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 95 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758283416 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000758283416 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758283416/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758283416/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758283416 Building ZINC000758283416 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758283416' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758283416 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000758283416 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758283416/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758283416 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 734) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/734: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)c1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)sc2c1-c1ccccc1CCC2) `ZINC000758283416.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000758283416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758283416/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000758283416 none NC(=O)c1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)sc2c1-c1ccccc1CCC2 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 24, 29, 15, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 15, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 29, 29, 4, 8, 8, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 95 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758283416 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758283416/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758283416 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 735) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/735: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)c1c(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)sc2c1-c1ccccc1CCC2) `ZINC000758283416.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000758283416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758283416/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000758283416 none NC(=O)c1c(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)sc2c1-c1ccccc1CCC2 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 24, 29, 15, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 15, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 29, 29, 4, 8, 8, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 95 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758283416 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000758283416 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758283416/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758283416/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758283416 Building ZINC000758308595 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758308595' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758308595 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000758308595 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758308595/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758308595 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 736) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/736 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/736' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCc1ccc2c(c1)CCCN2C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000758308595.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000758308595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758308595/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC000758308595 none CC(C)(C)OC(=O)NCc1ccc2c(c1)CCCN2C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 38, 30, 38, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 2, 2, 2, 2, 40, 40, 40, 40, 40, 40, 40, 40, 40, 30, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758308595 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758308595/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758308595 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 737) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/737 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/737' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCc1ccc2c(c1)CCCN2C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000758308595.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000758308595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758308595/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC000758308595 none CC(C)(C)OC(=O)NCc1ccc2c(c1)CCCN2C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 41, 40, 32, 40, 13, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 4, 1, 1, 1, 2, 2, 2, 2, 2, 41, 41, 41, 41, 41, 41, 41, 41, 41, 32, 13, 13, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758308595 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000758308595 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758308595/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758308595/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758308595 Building ZINC000758308595 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758308595' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758308595 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000758308595 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758308595/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758308595 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 736) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/736: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCc1ccc2c(c1)CCCN2C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000758308595.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000758308595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758308595/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC000758308595 none CC(C)(C)OC(=O)NCc1ccc2c(c1)CCCN2C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 38, 30, 38, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 2, 2, 2, 2, 40, 40, 40, 40, 40, 40, 40, 40, 40, 30, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758308595 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758308595/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758308595 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 737) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/737: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCc1ccc2c(c1)CCCN2C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000758308595.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000758308595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758308595/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC000758308595 none CC(C)(C)OC(=O)NCc1ccc2c(c1)CCCN2C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 41, 40, 32, 40, 13, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 4, 1, 1, 1, 2, 2, 2, 2, 2, 41, 41, 41, 41, 41, 41, 41, 41, 41, 32, 13, 13, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758308595 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000758308595 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758308595/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758308595/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758308595 Building ZINC000758427006 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758427006' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758427006 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000758427006 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758427006/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758427006 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 738) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/738 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/738' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCc1ccccc1)C(=O)c1ccccc1N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000758427006.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000758427006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758427006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000758427006 none CN(CCc1ccccc1)C(=O)c1ccccc1N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 21, 30, 30, 30, 30, 30, 30, 30, 10, 12, 10, 10, 10, 10, 10, 3, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 21, 21, 21, 30, 30, 30, 30, 30, 30, 30, 30, 30, 10, 10, 10, 10, 3, 3, 3, 4, 4] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758427006 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758427006/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758427006 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 739) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/739 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/739' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCc1ccccc1)C(=O)c1ccccc1N(C)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000758427006.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000758427006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758427006/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000758427006 none CN(CCc1ccccc1)C(=O)c1ccccc1N(C)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 22, 30, 30, 30, 30, 30, 30, 30, 10, 13, 10, 10, 10, 10, 10, 3, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 22, 22, 22, 30, 30, 30, 30, 30, 30, 30, 30, 30, 10, 10, 10, 10, 3, 3, 3, 4, 4] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758427006 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000758427006 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758427006/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758427006/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758427006 Building ZINC000758427006 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758427006' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758427006 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000758427006 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758427006/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758427006 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 738) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/738: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCc1ccccc1)C(=O)c1ccccc1N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000758427006.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000758427006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758427006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000758427006 none CN(CCc1ccccc1)C(=O)c1ccccc1N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 21, 30, 30, 30, 30, 30, 30, 30, 10, 12, 10, 10, 10, 10, 10, 3, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 21, 21, 21, 30, 30, 30, 30, 30, 30, 30, 30, 30, 10, 10, 10, 10, 3, 3, 3, 4, 4] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758427006 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758427006/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758427006 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 739) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/739: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCc1ccccc1)C(=O)c1ccccc1N(C)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000758427006.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000758427006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758427006/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000758427006 none CN(CCc1ccccc1)C(=O)c1ccccc1N(C)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 22, 30, 30, 30, 30, 30, 30, 30, 10, 13, 10, 10, 10, 10, 10, 3, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 22, 22, 22, 30, 30, 30, 30, 30, 30, 30, 30, 30, 10, 10, 10, 10, 3, 3, 3, 4, 4] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758427006 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000758427006 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758427006/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758427006/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758427006 Building ZINC000758905544 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758905544' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758905544 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000758905544 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758905544/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758905544 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 740) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/740 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/740' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)Nc1ccc(Br)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000758905544.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000758905544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758905544/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000758905544 none CCOC(=O)Nc1ccc(Br)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 17, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 31, 29, 20, 29, 13, 13, 13, 6, 13, 13, 13, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 41, 41, 41, 41, 41, 20, 13, 13, 13, 3, 6, 6] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758905544 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758905544/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758905544 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 741) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/741 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/741' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)Nc1ccc(Br)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000758905544.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000758905544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758905544/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000758905544 none CCOC(=O)Nc1ccc(Br)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 17, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 32, 30, 22, 30, 13, 13, 13, 3, 13, 13, 13, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 41, 41, 41, 41, 41, 22, 13, 13, 13, 3, 6, 6] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758905544 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000758905544 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758905544/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758905544/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758905544 Building ZINC000758905544 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758905544' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758905544 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000758905544 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758905544/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758905544 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 740) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/740: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)Nc1ccc(Br)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000758905544.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000758905544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758905544/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000758905544 none CCOC(=O)Nc1ccc(Br)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 17, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 31, 29, 20, 29, 13, 13, 13, 6, 13, 13, 13, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 41, 41, 41, 41, 41, 20, 13, 13, 13, 3, 6, 6] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758905544 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758905544/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758905544 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 741) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/741: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)Nc1ccc(Br)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000758905544.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000758905544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758905544/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000758905544 none CCOC(=O)Nc1ccc(Br)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 17, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 32, 30, 22, 30, 13, 13, 13, 3, 13, 13, 13, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 41, 41, 41, 41, 41, 22, 13, 13, 13, 3, 6, 6] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758905544 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000758905544 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758905544/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758905544/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000758905544 Building ZINC000781646915 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000781646915 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 742) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/742 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/742' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)cc2C(F)(F)F)CC1) `ZINC000781646915.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000781646915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000781646915 none CO[C@H]1CC[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)cc2C(F)(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 5, 15, 15, 15, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 12, 19, 19, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 19, 19, 19, 19, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 3, 2, 2, 2, 2, 2, 2, 19, 50, 50, 50, 50] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 743) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/743 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/743' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)cc2C(F)(F)F)CC1) `ZINC000781646915.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000781646915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000781646915 none CO[C@H]1CC[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)cc2C(F)(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 5, 15, 15, 15, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 48, 48, 15, 3, 20, 20, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 20, 20, 20, 20, 20, 20, 48, 48, 50, 50, 50, 49, 48, 48, 48, 20, 20, 3, 2, 2, 2, 2, 2, 2, 20, 48, 48, 48, 50] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 744) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/744 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/744' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)cc2C(F)(F)F)CC1) `ZINC000781646915.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000781646915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000781646915 none CO[C@H]1CC[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)cc2C(F)(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 5, 15, 15, 15, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 12, 19, 19, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 19, 19, 19, 19, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 3, 2, 2, 2, 2, 2, 2, 19, 50, 50, 50, 50] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 745) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/745 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/745' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)cc2C(F)(F)F)CC1) `ZINC000781646915.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000781646915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000781646915 none CO[C@H]1CC[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)cc2C(F)(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 5, 15, 15, 15, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 48, 48, 48, 48, 10, 3, 20, 20, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 20, 20, 20, 20, 20, 20, 48, 48, 50, 50, 50, 48, 48, 48, 48, 20, 20, 3, 2, 2, 2, 2, 2, 2, 20, 48, 48, 48, 48] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000781646915 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915 Building ZINC000781646915 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000781646915 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 742) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/742: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)cc2C(F)(F)F)CC1) `ZINC000781646915.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000781646915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000781646915 none CO[C@H]1CC[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)cc2C(F)(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 5, 15, 15, 15, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 12, 19, 19, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 19, 19, 19, 19, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 3, 2, 2, 2, 2, 2, 2, 19, 50, 50, 50, 50] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 743) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/743: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)cc2C(F)(F)F)CC1) `ZINC000781646915.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000781646915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000781646915 none CO[C@H]1CC[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)cc2C(F)(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 5, 15, 15, 15, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 48, 48, 15, 3, 20, 20, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 20, 20, 20, 20, 20, 20, 48, 48, 50, 50, 50, 49, 48, 48, 48, 20, 20, 3, 2, 2, 2, 2, 2, 2, 20, 48, 48, 48, 50] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 744) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/744: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)cc2C(F)(F)F)CC1) `ZINC000781646915.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000781646915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000781646915 none CO[C@H]1CC[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)cc2C(F)(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 5, 15, 15, 15, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 12, 19, 19, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 19, 19, 19, 19, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 3, 2, 2, 2, 2, 2, 2, 19, 50, 50, 50, 50] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 745) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/745: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)cc2C(F)(F)F)CC1) `ZINC000781646915.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000781646915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000781646915 none CO[C@H]1CC[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)cc2C(F)(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 5, 15, 15, 15, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 48, 48, 48, 48, 10, 3, 20, 20, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 20, 20, 20, 20, 20, 20, 48, 48, 50, 50, 50, 48, 48, 48, 48, 20, 20, 3, 2, 2, 2, 2, 2, 2, 20, 48, 48, 48, 48] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000781646915 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915 Building ZINC000781646915 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000781646915 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 742) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/742: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)cc2C(F)(F)F)CC1) `ZINC000781646915.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000781646915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000781646915 none CO[C@H]1CC[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)cc2C(F)(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 5, 15, 15, 15, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 12, 19, 19, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 19, 19, 19, 19, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 3, 2, 2, 2, 2, 2, 2, 19, 50, 50, 50, 50] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 743) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/743: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)cc2C(F)(F)F)CC1) `ZINC000781646915.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000781646915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000781646915 none CO[C@H]1CC[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)cc2C(F)(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 5, 15, 15, 15, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 48, 48, 15, 3, 20, 20, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 20, 20, 20, 20, 20, 20, 48, 48, 50, 50, 50, 49, 48, 48, 48, 20, 20, 3, 2, 2, 2, 2, 2, 2, 20, 48, 48, 48, 50] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 744) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/744: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)cc2C(F)(F)F)CC1) `ZINC000781646915.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000781646915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000781646915 none CO[C@H]1CC[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)cc2C(F)(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 5, 15, 15, 15, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 12, 19, 19, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 19, 19, 19, 19, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 3, 2, 2, 2, 2, 2, 2, 19, 50, 50, 50, 50] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 745) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/745: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)cc2C(F)(F)F)CC1) `ZINC000781646915.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000781646915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000781646915 none CO[C@H]1CC[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)cc2C(F)(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 5, 15, 15, 15, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 48, 48, 48, 48, 10, 3, 20, 20, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 20, 20, 20, 20, 20, 20, 48, 48, 50, 50, 50, 48, 48, 48, 48, 20, 20, 3, 2, 2, 2, 2, 2, 2, 20, 48, 48, 48, 48] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000781646915 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915 Building ZINC000781646915 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000781646915 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 742) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/742: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)cc2C(F)(F)F)CC1) `ZINC000781646915.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000781646915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000781646915 none CO[C@H]1CC[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)cc2C(F)(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 5, 15, 15, 15, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 12, 19, 19, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 19, 19, 19, 19, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 3, 2, 2, 2, 2, 2, 2, 19, 50, 50, 50, 50] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 743) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/743: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)cc2C(F)(F)F)CC1) `ZINC000781646915.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000781646915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000781646915 none CO[C@H]1CC[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)cc2C(F)(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 5, 15, 15, 15, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 48, 48, 15, 3, 20, 20, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 20, 20, 20, 20, 20, 20, 48, 48, 50, 50, 50, 49, 48, 48, 48, 20, 20, 3, 2, 2, 2, 2, 2, 2, 20, 48, 48, 48, 50] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 744) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/744: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)cc2C(F)(F)F)CC1) `ZINC000781646915.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000781646915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000781646915 none CO[C@H]1CC[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)cc2C(F)(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 5, 15, 15, 15, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 12, 19, 19, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 19, 19, 19, 19, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 3, 2, 2, 2, 2, 2, 2, 19, 50, 50, 50, 50] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 745) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/745: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)cc2C(F)(F)F)CC1) `ZINC000781646915.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000781646915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000781646915 none CO[C@H]1CC[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)cc2C(F)(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 5, 15, 15, 15, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 48, 48, 48, 48, 10, 3, 20, 20, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 20, 20, 20, 20, 20, 20, 48, 48, 50, 50, 50, 48, 48, 48, 48, 20, 20, 3, 2, 2, 2, 2, 2, 2, 20, 48, 48, 48, 48] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000781646915 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000781646915 Building ZINC000784534549 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000784534549' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000784534549 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000784534549 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000784534549/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000784534549 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 746) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/746 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/746' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](c2cccc(C(F)(F)F)c2)C1) `ZINC000784534549.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000784534549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000784534549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000784534549 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](c2cccc(C(F)(F)F)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 6, 10, 10, 3, 3, 1, 1, 1, 1, 2, 3, 4, 4, 4, 4, 4, 20, 20, 7, 20, 20, 20, 20, 20, 20, 4, 3, 3, 3, 10, 10, 10, 10, 10, 3, 3, 3, 4, 4, 4, 4, 20, 20, 7, 20, 4, 4] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 79 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000784534549 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000784534549/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000784534549 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 747) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/747 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/747' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](c2cccc(C(F)(F)F)c2)C1) `ZINC000784534549.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000784534549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000784534549/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000784534549 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](c2cccc(C(F)(F)F)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 3, 11, 11, 3, 3, 1, 1, 1, 1, 2, 3, 6, 6, 6, 6, 6, 28, 28, 7, 28, 28, 28, 28, 28, 28, 6, 3, 3, 3, 11, 11, 3, 11, 11, 3, 3, 3, 6, 6, 6, 6, 28, 28, 11, 28, 6, 6] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 102 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000784534549 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000784534549 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000784534549/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000784534549/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000784534549 Building ZINC000784534549 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000784534549' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000784534549 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000784534549 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000784534549/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000784534549 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 746) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/746: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](c2cccc(C(F)(F)F)c2)C1) `ZINC000784534549.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000784534549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000784534549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000784534549 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](c2cccc(C(F)(F)F)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 6, 10, 10, 3, 3, 1, 1, 1, 1, 2, 3, 4, 4, 4, 4, 4, 20, 20, 7, 20, 20, 20, 20, 20, 20, 4, 3, 3, 3, 10, 10, 10, 10, 10, 3, 3, 3, 4, 4, 4, 4, 20, 20, 7, 20, 4, 4] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 79 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000784534549 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000784534549/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000784534549 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 747) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/747: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](c2cccc(C(F)(F)F)c2)C1) `ZINC000784534549.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000784534549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000784534549/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000784534549 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](c2cccc(C(F)(F)F)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 3, 11, 11, 3, 3, 1, 1, 1, 1, 2, 3, 6, 6, 6, 6, 6, 28, 28, 7, 28, 28, 28, 28, 28, 28, 6, 3, 3, 3, 11, 11, 3, 11, 11, 3, 3, 3, 6, 6, 6, 6, 28, 28, 11, 28, 6, 6] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 102 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000784534549 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000784534549 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000784534549/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000784534549/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000784534549 Building ZINC000784534560 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000784534560' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000784534560 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000784534560 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000784534560/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000784534560 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 748) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/748 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/748' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](c2cccc(C(F)(F)F)c2)C1) `ZINC000784534560.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000784534560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000784534560/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000784534560 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](c2cccc(C(F)(F)F)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 2, 4, 6, 6, 6, 6, 6, 25, 25, 6, 25, 25, 25, 25, 25, 25, 6, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 6, 6, 6, 6, 25, 25, 6, 25, 6, 6] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 83 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000784534560 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000784534560/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000784534560 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 749) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/749 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/749' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](c2cccc(C(F)(F)F)c2)C1) `ZINC000784534560.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000784534560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000784534560/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000784534560 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](c2cccc(C(F)(F)F)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 4, 8, 8, 2, 2, 1, 1, 1, 1, 2, 3, 4, 4, 4, 4, 4, 22, 22, 4, 22, 22, 22, 22, 22, 22, 4, 2, 2, 2, 8, 8, 8, 8, 8, 2, 2, 2, 4, 4, 4, 4, 22, 22, 4, 22, 4, 4] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 86 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000784534560 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000784534560 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000784534560/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000784534560/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000784534560 Building ZINC000784534560 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000784534560' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000784534560 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000784534560 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000784534560/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000784534560 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 748) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/748: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](c2cccc(C(F)(F)F)c2)C1) `ZINC000784534560.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000784534560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000784534560/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000784534560 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](c2cccc(C(F)(F)F)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 2, 4, 6, 6, 6, 6, 6, 25, 25, 6, 25, 25, 25, 25, 25, 25, 6, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 6, 6, 6, 6, 25, 25, 6, 25, 6, 6] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 83 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000784534560 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000784534560/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000784534560 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 749) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/749: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](c2cccc(C(F)(F)F)c2)C1) `ZINC000784534560.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000784534560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000784534560/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000784534560 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](c2cccc(C(F)(F)F)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 4, 8, 8, 2, 2, 1, 1, 1, 1, 2, 3, 4, 4, 4, 4, 4, 22, 22, 4, 22, 22, 22, 22, 22, 22, 4, 2, 2, 2, 8, 8, 8, 8, 8, 2, 2, 2, 4, 4, 4, 4, 22, 22, 4, 22, 4, 4] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 86 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000784534560 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000784534560 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000784534560/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000784534560/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000784534560 Building ZINC001116779136 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001116779136' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001116779136 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001116779136 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001116779136/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001116779136 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 750) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/750 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/750' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)c2ccc(OC)cc2OC)cc1) `ZINC001116779136.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001116779136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001116779136/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001116779136 none COc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)c2ccc(OC)cc2OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 1, 12, 5, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 12, 16, 16, 6, 4, 6, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 6, 10, 10, 6, 10, 16, 10, 10, 10, 13, 16, 16, 16, 16, 16, 16, 16, 4, 8, 8, 10, 10, 16, 16, 16, 10, 13, 13, 13, 16, 16] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 105 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001116779136 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001116779136/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001116779136 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 751) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/751 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/751' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)c2ccc(OC)cc2OC)cc1) `ZINC001116779136.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001116779136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001116779136/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001116779136 none COc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)c2ccc(OC)cc2OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 1, 12, 5, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 7, 17, 17, 7, 4, 7, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 7, 12, 12, 7, 12, 20, 12, 12, 12, 16, 17, 17, 17, 17, 17, 17, 17, 4, 6, 6, 12, 12, 20, 20, 20, 12, 16, 16, 16, 17, 17] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 143 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001116779136 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001116779136 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001116779136/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001116779136/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001116779136 Building ZINC001116779136 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001116779136' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001116779136 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001116779136 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001116779136/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001116779136 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 750) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/750: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)c2ccc(OC)cc2OC)cc1) `ZINC001116779136.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001116779136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001116779136/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001116779136 none COc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)c2ccc(OC)cc2OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 1, 12, 5, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 12, 16, 16, 6, 4, 6, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 6, 10, 10, 6, 10, 16, 10, 10, 10, 13, 16, 16, 16, 16, 16, 16, 16, 4, 8, 8, 10, 10, 16, 16, 16, 10, 13, 13, 13, 16, 16] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 105 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001116779136 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001116779136/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001116779136 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 751) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/751: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)c2ccc(OC)cc2OC)cc1) `ZINC001116779136.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001116779136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001116779136/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001116779136 none COc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)c2ccc(OC)cc2OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 1, 12, 5, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 7, 17, 17, 7, 4, 7, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 7, 12, 12, 7, 12, 20, 12, 12, 12, 16, 17, 17, 17, 17, 17, 17, 17, 4, 6, 6, 12, 12, 20, 20, 20, 12, 16, 16, 16, 17, 17] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 143 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001116779136 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001116779136 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001116779136/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001116779136/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001116779136 Building ZINC001116779137 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001116779137' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001116779137 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001116779137 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001116779137/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001116779137 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 752) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/752 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/752' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)c2ccc(OC)cc2OC)cc1) `ZINC001116779137.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001116779137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001116779137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001116779137 none COc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)c2ccc(OC)cc2OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 1, 12, 5, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 6, 3, 6, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 11, 11, 6, 11, 20, 11, 11, 11, 15, 16, 16, 16, 16, 16, 16, 16, 3, 6, 6, 11, 11, 20, 20, 20, 11, 15, 15, 15, 16, 16] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 103 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001116779137 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001116779137/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001116779137 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 753) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/753 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/753' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)c2ccc(OC)cc2OC)cc1) `ZINC001116779137.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001116779137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001116779137/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001116779137 none COc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)c2ccc(OC)cc2OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 1, 12, 5, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 15, 15, 6, 4, 6, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 6, 10, 10, 10, 10, 17, 10, 10, 10, 14, 15, 15, 15, 15, 15, 15, 15, 4, 8, 8, 10, 10, 17, 17, 17, 10, 14, 14, 14, 15, 15] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 107 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001116779137 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001116779137 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001116779137/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001116779137/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001116779137 Building ZINC001116779137 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001116779137' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001116779137 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001116779137 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001116779137/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001116779137 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 752) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/752: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)c2ccc(OC)cc2OC)cc1) `ZINC001116779137.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001116779137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001116779137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001116779137 none COc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)c2ccc(OC)cc2OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 1, 12, 5, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 6, 3, 6, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 11, 11, 6, 11, 20, 11, 11, 11, 15, 16, 16, 16, 16, 16, 16, 16, 3, 6, 6, 11, 11, 20, 20, 20, 11, 15, 15, 15, 16, 16] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 103 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001116779137 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001116779137/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001116779137 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 753) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/753: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)c2ccc(OC)cc2OC)cc1) `ZINC001116779137.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001116779137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001116779137/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001116779137 none COc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)c2ccc(OC)cc2OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 1, 12, 5, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 15, 15, 6, 4, 6, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 6, 10, 10, 10, 10, 17, 10, 10, 10, 14, 15, 15, 15, 15, 15, 15, 15, 4, 8, 8, 10, 10, 17, 17, 17, 10, 14, 14, 14, 15, 15] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 107 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001116779137 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001116779137 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001116779137/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001116779137/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001116779137 Building ZINC000117262427 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000117262427' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000117262427 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000117262427 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000117262427/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000117262427 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 754) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/754 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/754' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Oc2cccc(F)c2)nc1) `ZINC000117262427.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000117262427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000117262427/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000117262427 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Oc2cccc(F)c2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 4, 4, 3, 4, 4, 3, 3, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 22, 44, 44, 44, 44, 44, 44, 7, 7, 3, 3, 3, 4, 4, 3, 4, 4, 3, 3, 3, 2, 7, 7, 44, 44, 44, 44, 7] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000117262427 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000117262427/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000117262427 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 755) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/755 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/755' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(Oc2cccc(F)c2)nc1) `ZINC000117262427.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000117262427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000117262427/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000117262427 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(Oc2cccc(F)c2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 24, 48, 48, 48, 48, 48, 48, 7, 7, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 7, 7, 48, 48, 48, 48, 7] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000117262427 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000117262427 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000117262427/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000117262427/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000117262427 Building ZINC000117262427 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000117262427' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000117262427 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000117262427 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000117262427/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000117262427 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 754) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/754: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Oc2cccc(F)c2)nc1) `ZINC000117262427.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000117262427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000117262427/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000117262427 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Oc2cccc(F)c2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 4, 4, 3, 4, 4, 3, 3, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 22, 44, 44, 44, 44, 44, 44, 7, 7, 3, 3, 3, 4, 4, 3, 4, 4, 3, 3, 3, 2, 7, 7, 44, 44, 44, 44, 7] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000117262427 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000117262427/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000117262427 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 755) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/755: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(Oc2cccc(F)c2)nc1) `ZINC000117262427.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000117262427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000117262427/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000117262427 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(Oc2cccc(F)c2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 24, 48, 48, 48, 48, 48, 48, 7, 7, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 7, 7, 48, 48, 48, 48, 7] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000117262427 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC000117262427 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000117262427/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000117262427/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC000117262427 Building ZINC001142278996 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142278996' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142278996 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142278996 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142278996/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142278996 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 756) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/756 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/756' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1nc(c2cccc3ccccc32)c2c1ncnc2NC(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142278996.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142278996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142278996/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001142278996 none CC(C)(C)n1nc(c2cccc3ccccc32)c2c1ncnc2NC(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 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] 0 hydrogens 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, 9, 15, 15, 9, 9, 9, 9, 24, 24, 24, 24, 24, 24, 24, 24, 24, 9, 9, 9, 9, 9, 4, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 24, 24, 24, 24, 24, 24, 24, 9, 4, 10, 10, 10] 50 rigid atoms, others: [24, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142278996 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142278996/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142278996 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 757) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/757 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/757' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1nc(c2cccc3ccccc32)c2c1ncnc2NC(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142278996.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142278996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142278996/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001142278996 none CC(C)(C)n1nc(c2cccc3ccccc32)c2c1ncnc2NC(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 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] 0 hydrogens 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, 17, 17, 9, 9, 9, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 9, 9, 9, 9, 4, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 17, 17, 17, 17, 17, 17, 17, 17, 17, 23, 23, 23, 23, 23, 23, 23, 9, 4, 10, 10, 10] 50 rigid atoms, others: [24, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142278996 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001142278996 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142278996/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142278996/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142278996 Building ZINC001142278996 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142278996' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142278996 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142278996 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142278996/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142278996 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 756) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/756: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1nc(c2cccc3ccccc32)c2c1ncnc2NC(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142278996.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142278996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142278996/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001142278996 none CC(C)(C)n1nc(c2cccc3ccccc32)c2c1ncnc2NC(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 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] 0 hydrogens 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, 9, 15, 15, 9, 9, 9, 9, 24, 24, 24, 24, 24, 24, 24, 24, 24, 9, 9, 9, 9, 9, 4, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 24, 24, 24, 24, 24, 24, 24, 9, 4, 10, 10, 10] 50 rigid atoms, others: [24, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142278996 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142278996/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142278996 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 757) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/757: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1nc(c2cccc3ccccc32)c2c1ncnc2NC(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142278996.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142278996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142278996/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001142278996 none CC(C)(C)n1nc(c2cccc3ccccc32)c2c1ncnc2NC(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 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] 0 hydrogens 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, 17, 17, 9, 9, 9, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 9, 9, 9, 9, 4, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 17, 17, 17, 17, 17, 17, 17, 17, 17, 23, 23, 23, 23, 23, 23, 23, 9, 4, 10, 10, 10] 50 rigid atoms, others: [24, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142278996 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001142278996 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142278996/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142278996/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142278996 Building ZINC001142284081 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142284081' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142284081 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142284081 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142284081/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142284081 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 758) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/758 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/758' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(CN(C(=O)[C@]([O-])([SiH3])c2ccco2)[C@H]2CC[C@H](NC(=O)OC(C)(C)C)CC2)cc1) `ZINC001142284081.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142284081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142284081/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001142284081 none Cc1ccc(CN(C(=O)[C@]([O-])([SiH3])c2ccco2)[C@H]2CC[C@H](NC(=O)OC(C)(C)C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 7, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 8, 9, 9, 7, 5, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 16, 24, 24, 32, 32, 32, 32, 5, 5, 9, 9, 9, 9, 9, 9, 9, 7, 7, 5, 5, 5, 5, 5, 5, 5, 16, 32, 32, 32, 32, 32, 32, 32, 32, 32, 5, 5, 5, 5, 9, 9] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142284081 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142284081/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142284081 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 759) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/759 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/759' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2ccco2)[C@H]2CC[C@H](NC(=O)OC(C)(C)C)CC2)cc1) `ZINC001142284081.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142284081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142284081/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001142284081 none Cc1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2ccco2)[C@H]2CC[C@H](NC(=O)OC(C)(C)C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 7, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 8, 9, 9, 7, 5, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 16, 24, 24, 33, 33, 33, 33, 5, 5, 9, 9, 9, 9, 9, 9, 9, 7, 7, 4, 4, 4, 5, 5, 5, 5, 16, 33, 33, 33, 33, 33, 33, 33, 33, 33, 5, 5, 5, 5, 9, 9] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142284081 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001142284081 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142284081/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142284081/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142284081 Building ZINC001142284081 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142284081' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142284081 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142284081 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142284081/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142284081 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 758) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/758: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(CN(C(=O)[C@]([O-])([SiH3])c2ccco2)[C@H]2CC[C@H](NC(=O)OC(C)(C)C)CC2)cc1) `ZINC001142284081.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142284081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142284081/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001142284081 none Cc1ccc(CN(C(=O)[C@]([O-])([SiH3])c2ccco2)[C@H]2CC[C@H](NC(=O)OC(C)(C)C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 7, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 8, 9, 9, 7, 5, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 16, 24, 24, 32, 32, 32, 32, 5, 5, 9, 9, 9, 9, 9, 9, 9, 7, 7, 5, 5, 5, 5, 5, 5, 5, 16, 32, 32, 32, 32, 32, 32, 32, 32, 32, 5, 5, 5, 5, 9, 9] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142284081 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142284081/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142284081 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 759) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/759: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2ccco2)[C@H]2CC[C@H](NC(=O)OC(C)(C)C)CC2)cc1) `ZINC001142284081.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142284081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142284081/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001142284081 none Cc1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2ccco2)[C@H]2CC[C@H](NC(=O)OC(C)(C)C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 7, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 8, 9, 9, 7, 5, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 16, 24, 24, 33, 33, 33, 33, 5, 5, 9, 9, 9, 9, 9, 9, 9, 7, 7, 4, 4, 4, 5, 5, 5, 5, 16, 33, 33, 33, 33, 33, 33, 33, 33, 33, 5, 5, 5, 5, 9, 9] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142284081 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001142284081 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142284081/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142284081/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142284081 Building ZINC001142684200 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142684200' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142684200 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142684200 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142684200/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142684200 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 760) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/760 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/760' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C(=O)c2oc3ccccc3c2NC(=O)[C@@]([O-])([SiH3])c2ccccc2)cc1OC) `ZINC001142684200.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142684200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142684200/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001142684200 none COc1ccc(C(=O)c2oc3ccccc3c2NC(=O)[C@@]([O-])([SiH3])c2ccccc2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 8, 10, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 27, 27, 27, 50, 50, 50, 50, 27, 27, 8, 8, 8, 8, 3, 2, 2, 1, 2, 2, 27, 50, 50, 50] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142684200 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142684200/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142684200 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 761) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/761 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/761' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C(=O)c2oc3ccccc3c2NC(=O)[C@]([O-])([SiH3])c2ccccc2)cc1OC) `ZINC001142684200.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142684200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142684200/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001142684200 none COc1ccc(C(=O)c2oc3ccccc3c2NC(=O)[C@]([O-])([SiH3])c2ccccc2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 8, 10, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 27, 27, 27, 50, 50, 50, 50, 27, 27, 8, 8, 8, 8, 3, 2, 2, 1, 2, 2, 27, 50, 50, 50] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142684200 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001142684200 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142684200/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142684200/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142684200 Building ZINC001142684200 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142684200' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142684200 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142684200 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142684200/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142684200 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 760) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/760: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C(=O)c2oc3ccccc3c2NC(=O)[C@@]([O-])([SiH3])c2ccccc2)cc1OC) `ZINC001142684200.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142684200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142684200/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001142684200 none COc1ccc(C(=O)c2oc3ccccc3c2NC(=O)[C@@]([O-])([SiH3])c2ccccc2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 8, 10, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 27, 27, 27, 50, 50, 50, 50, 27, 27, 8, 8, 8, 8, 3, 2, 2, 1, 2, 2, 27, 50, 50, 50] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142684200 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142684200/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142684200 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 761) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/761: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C(=O)c2oc3ccccc3c2NC(=O)[C@]([O-])([SiH3])c2ccccc2)cc1OC) `ZINC001142684200.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142684200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142684200/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001142684200 none COc1ccc(C(=O)c2oc3ccccc3c2NC(=O)[C@]([O-])([SiH3])c2ccccc2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 8, 10, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 27, 27, 27, 50, 50, 50, 50, 27, 27, 8, 8, 8, 8, 3, 2, 2, 1, 2, 2, 27, 50, 50, 50] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142684200 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001142684200 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142684200/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142684200/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142684200 Building ZINC001142684203 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142684203' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142684203 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142684203 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142684203/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142684203 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 762) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/762 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/762' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ncnc2[nH]nc(c3ccc(Oc4ccccc4)cc3)c21)[C@]([O-])([SiH3])c1ccccc1) `ZINC001142684203.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142684203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142684203/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001142684203 none O=C(Nc1ncnc2[nH]nc(c3ccc(Oc4ccccc4)cc3)c21)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 8, 1, 8, 6, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 13, 13, 7, 10, 48, 50, 50, 48, 50, 50, 13, 13, 7, 1, 1, 1, 3, 3, 1, 3, 3, 3, 7, 13, 13, 50, 50, 48, 50, 50, 13, 13, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142684203 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142684203/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142684203 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 763) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/763 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/763' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ncnc2[nH]nc(c3ccc(Oc4ccccc4)cc3)c21)[C@@]([O-])([SiH3])c1ccccc1) `ZINC001142684203.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142684203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142684203/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001142684203 none O=C(Nc1ncnc2[nH]nc(c3ccc(Oc4ccccc4)cc3)c21)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 8, 1, 8, 6, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 6, 9, 47, 50, 50, 47, 50, 50, 12, 12, 6, 1, 1, 1, 3, 3, 1, 3, 3, 2, 6, 12, 12, 50, 50, 47, 50, 50, 12, 12, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142684203 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001142684203 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142684203/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142684203/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142684203 Building ZINC001142684203 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142684203' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142684203 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142684203 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142684203/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142684203 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 762) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/762: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ncnc2[nH]nc(c3ccc(Oc4ccccc4)cc3)c21)[C@]([O-])([SiH3])c1ccccc1) `ZINC001142684203.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142684203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142684203/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001142684203 none O=C(Nc1ncnc2[nH]nc(c3ccc(Oc4ccccc4)cc3)c21)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 8, 1, 8, 6, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 13, 13, 7, 10, 48, 50, 50, 48, 50, 50, 13, 13, 7, 1, 1, 1, 3, 3, 1, 3, 3, 3, 7, 13, 13, 50, 50, 48, 50, 50, 13, 13, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142684203 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142684203/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142684203 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 763) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/763: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ncnc2[nH]nc(c3ccc(Oc4ccccc4)cc3)c21)[C@@]([O-])([SiH3])c1ccccc1) `ZINC001142684203.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142684203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142684203/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001142684203 none O=C(Nc1ncnc2[nH]nc(c3ccc(Oc4ccccc4)cc3)c21)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 8, 1, 8, 6, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 6, 9, 47, 50, 50, 47, 50, 50, 12, 12, 6, 1, 1, 1, 3, 3, 1, 3, 3, 2, 6, 12, 12, 50, 50, 47, 50, 50, 12, 12, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142684203 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001142684203 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142684203/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142684203/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142684203 Building ZINC001142685643 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142685643' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142685643 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142685643 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142685643/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142685643 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 764) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/764 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/764' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(O[C@@H](c2ccc(Cl)cc2)c2ccccn2)CC1)[C@]([O-])([SiH3])c1ccccc1) `ZINC001142685643.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142685643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142685643/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001142685643 none O=C(N1CCC(O[C@@H](c2ccc(Cl)cc2)c2ccccn2)CC1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 5, 7, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 5, 5, 5, 5, 19, 47, 47, 47, 47, 47, 47, 47, 47, 47, 50, 50, 50, 50, 50, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 47, 47, 47, 47, 50, 50, 50, 50, 5, 5, 5, 5, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 49, 50, 51, 52, 53, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 161 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142685643 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142685643/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142685643 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 765) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/765 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/765' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(O[C@@H](c2ccc(Cl)cc2)c2ccccn2)CC1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC001142685643.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142685643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142685643/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001142685643 none O=C(N1CCC(O[C@@H](c2ccc(Cl)cc2)c2ccccn2)CC1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 5, 7, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 4, 4, 4, 4, 17, 46, 46, 46, 46, 46, 46, 46, 46, 46, 50, 50, 50, 50, 50, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 46, 46, 46, 46, 50, 50, 50, 50, 4, 4, 4, 4, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 49, 50, 51, 52, 53, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 163 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142685643 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001142685643 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142685643/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142685643/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142685643 Building ZINC001142685643 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142685643' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142685643 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142685643 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142685643/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142685643 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 764) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/764: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(O[C@@H](c2ccc(Cl)cc2)c2ccccn2)CC1)[C@]([O-])([SiH3])c1ccccc1) `ZINC001142685643.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142685643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142685643/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001142685643 none O=C(N1CCC(O[C@@H](c2ccc(Cl)cc2)c2ccccn2)CC1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 5, 7, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 5, 5, 5, 5, 19, 47, 47, 47, 47, 47, 47, 47, 47, 47, 50, 50, 50, 50, 50, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 47, 47, 47, 47, 50, 50, 50, 50, 5, 5, 5, 5, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 49, 50, 51, 52, 53, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 161 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142685643 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142685643/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142685643 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 765) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/765: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(O[C@@H](c2ccc(Cl)cc2)c2ccccn2)CC1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC001142685643.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142685643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142685643/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001142685643 none O=C(N1CCC(O[C@@H](c2ccc(Cl)cc2)c2ccccn2)CC1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 5, 7, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 4, 4, 4, 4, 17, 46, 46, 46, 46, 46, 46, 46, 46, 46, 50, 50, 50, 50, 50, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 46, 46, 46, 46, 50, 50, 50, 50, 4, 4, 4, 4, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 49, 50, 51, 52, 53, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 163 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142685643 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001142685643 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142685643/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142685643/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142685643 Building ZINC001142685644 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142685644' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142685644 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142685644 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142685644/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142685644 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 766) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/766 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/766' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(O[C@H](c2ccc(Cl)cc2)c2ccccn2)CC1)[C@]([O-])([SiH3])c1ccccc1) `ZINC001142685644.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142685644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142685644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001142685644 none O=C(N1CCC(O[C@H](c2ccc(Cl)cc2)c2ccccn2)CC1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 5, 7, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 5, 5, 5, 5, 21, 47, 47, 47, 47, 47, 47, 47, 47, 47, 50, 50, 50, 50, 50, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 47, 47, 47, 47, 50, 50, 50, 50, 5, 5, 5, 5, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 49, 50, 51, 52, 53, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 151 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142685644 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142685644/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142685644 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 767) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/767 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/767' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(O[C@H](c2ccc(Cl)cc2)c2ccccn2)CC1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC001142685644.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142685644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142685644/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001142685644 none O=C(N1CCC(O[C@H](c2ccc(Cl)cc2)c2ccccn2)CC1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 5, 7, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 4, 4, 4, 4, 16, 44, 44, 44, 44, 44, 44, 44, 44, 44, 50, 50, 50, 50, 50, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 44, 44, 44, 44, 50, 50, 50, 50, 4, 4, 4, 4, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 49, 50, 51, 52, 53, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 162 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142685644 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001142685644 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142685644/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142685644/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142685644 Building ZINC001142685644 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142685644' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142685644 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142685644 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142685644/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142685644 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 766) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/766: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(O[C@H](c2ccc(Cl)cc2)c2ccccn2)CC1)[C@]([O-])([SiH3])c1ccccc1) `ZINC001142685644.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142685644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142685644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001142685644 none O=C(N1CCC(O[C@H](c2ccc(Cl)cc2)c2ccccn2)CC1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 5, 7, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 5, 5, 5, 5, 21, 47, 47, 47, 47, 47, 47, 47, 47, 47, 50, 50, 50, 50, 50, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 47, 47, 47, 47, 50, 50, 50, 50, 5, 5, 5, 5, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 49, 50, 51, 52, 53, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 151 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142685644 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142685644/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142685644 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 767) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/767: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(O[C@H](c2ccc(Cl)cc2)c2ccccn2)CC1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC001142685644.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142685644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142685644/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001142685644 none O=C(N1CCC(O[C@H](c2ccc(Cl)cc2)c2ccccn2)CC1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 5, 7, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 4, 4, 4, 4, 16, 44, 44, 44, 44, 44, 44, 44, 44, 44, 50, 50, 50, 50, 50, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 44, 44, 44, 44, 50, 50, 50, 50, 4, 4, 4, 4, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 49, 50, 51, 52, 53, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 162 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142685644 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001142685644 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142685644/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142685644/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142685644 Building ZINC001142686195 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142686195' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142686195 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142686195 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142686195/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142686195 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 768) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/768 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/768' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc2cc(C3CCN(C(=O)[C@@]([O-])([SiH3])c4ccccc4)CC3)oc2c(Br)c1) `ZINC001142686195.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142686195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142686195/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001142686195 none COc1cc2cc(C3CCN(C(=O)[C@@]([O-])([SiH3])c4ccccc4)CC3)oc2c(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 11, 11, 11, 11, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 46, 47]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142686195 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142686195/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142686195 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 769) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/769 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/769' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc2cc(C3CCN(C(=O)[C@]([O-])([SiH3])c4ccccc4)CC3)oc2c(Br)c1) `ZINC001142686195.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142686195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142686195/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001142686195 none COc1cc2cc(C3CCN(C(=O)[C@]([O-])([SiH3])c4ccccc4)CC3)oc2c(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 12, 12, 12, 12, 5, 2, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 46, 47]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142686195 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001142686195 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142686195/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142686195/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142686195 Building ZINC001142686195 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142686195' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142686195 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142686195 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142686195/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142686195 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 768) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/768: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc2cc(C3CCN(C(=O)[C@@]([O-])([SiH3])c4ccccc4)CC3)oc2c(Br)c1) `ZINC001142686195.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142686195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142686195/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001142686195 none COc1cc2cc(C3CCN(C(=O)[C@@]([O-])([SiH3])c4ccccc4)CC3)oc2c(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 11, 11, 11, 11, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 46, 47]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142686195 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142686195/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142686195 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 769) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/769: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc2cc(C3CCN(C(=O)[C@]([O-])([SiH3])c4ccccc4)CC3)oc2c(Br)c1) `ZINC001142686195.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142686195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142686195/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001142686195 none COc1cc2cc(C3CCN(C(=O)[C@]([O-])([SiH3])c4ccccc4)CC3)oc2c(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 12, 12, 12, 12, 5, 2, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 46, 47]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142686195 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001142686195 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142686195/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142686195/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142686195 Building ZINC001142687254 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142687254' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142687254 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142687254 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142687254/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142687254 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 770) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/770 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/770' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(C2=Nc3ccccc3Oc3ccc(Cl)cc32)CC1)[C@]([O-])([SiH3])c1ccccc1) `ZINC001142687254.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142687254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142687254/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001142687254 none O=C(N1CCN(C2=Nc3ccccc3Oc3ccc(Cl)cc32)CC1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 6, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 1, 1, 1, 2, 2, 1, 2, 2, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 2, 2, 1, 2, 2] 50 rigid atoms, others: [24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142687254 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142687254/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142687254 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 771) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/771 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/771' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(C2=Nc3ccccc3Oc3ccc(Cl)cc32)CC1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC001142687254.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142687254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142687254/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001142687254 none O=C(N1CCN(C2=Nc3ccccc3Oc3ccc(Cl)cc32)CC1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 6, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 13, 13, 1, 1, 1, 2, 2, 1, 2, 2, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 2, 2, 1, 2, 2] 50 rigid atoms, others: [24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142687254 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001142687254 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142687254/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142687254/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142687254 Building ZINC001142687254 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142687254' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142687254 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142687254 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142687254/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142687254 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 770) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/770: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(C2=Nc3ccccc3Oc3ccc(Cl)cc32)CC1)[C@]([O-])([SiH3])c1ccccc1) `ZINC001142687254.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142687254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142687254/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001142687254 none O=C(N1CCN(C2=Nc3ccccc3Oc3ccc(Cl)cc32)CC1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 6, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 1, 1, 1, 2, 2, 1, 2, 2, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 2, 2, 1, 2, 2] 50 rigid atoms, others: [24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142687254 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142687254/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142687254 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 771) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/771: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(C2=Nc3ccccc3Oc3ccc(Cl)cc32)CC1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC001142687254.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142687254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142687254/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001142687254 none O=C(N1CCN(C2=Nc3ccccc3Oc3ccc(Cl)cc32)CC1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 6, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 13, 13, 1, 1, 1, 2, 2, 1, 2, 2, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 2, 2, 1, 2, 2] 50 rigid atoms, others: [24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142687254 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001142687254 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142687254/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142687254/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142687254 Building ZINC001142688092 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142688092' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142688092 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142688092 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142688092/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142688092 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 772) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/772 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/772' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1ccc2ncnc(N(C(=O)[C@]([O-])([SiH3])c3ccccc3)c3cccc(Br)c3)c2c1) `ZINC001142688092.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142688092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142688092/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001142688092 none Nc1ccc2ncnc(N(C(=O)[C@]([O-])([SiH3])c3ccccc3)c3cccc(Br)c3)c2c1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 8, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 7, 7, 7, 3, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 23, 15, 6, 1, 6, 1, 1, 1, 2, 2, 1, 2, 2, 15, 42, 42, 42, 42, 42, 42, 23, 23, 23, 23, 23, 23, 23, 2, 2, 1, 2, 2, 42, 42, 42, 42, 23] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142688092 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142688092/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142688092 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 773) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/773 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/773' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1ccc2ncnc(N(C(=O)[C@@]([O-])([SiH3])c3ccccc3)c3cccc(Br)c3)c2c1) `ZINC001142688092.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142688092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142688092/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001142688092 none Nc1ccc2ncnc(N(C(=O)[C@@]([O-])([SiH3])c3ccccc3)c3cccc(Br)c3)c2c1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 8, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 7, 7, 7, 3, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 14, 6, 1, 6, 1, 1, 1, 2, 2, 1, 2, 2, 14, 42, 42, 32, 42, 42, 42, 22, 22, 22, 22, 22, 22, 22, 2, 2, 1, 2, 2, 42, 42, 39, 42, 22] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142688092 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001142688092 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142688092/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142688092/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142688092 Building ZINC001142688092 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142688092' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142688092 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142688092 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142688092/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142688092 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 772) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/772: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1ccc2ncnc(N(C(=O)[C@]([O-])([SiH3])c3ccccc3)c3cccc(Br)c3)c2c1) `ZINC001142688092.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142688092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142688092/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001142688092 none Nc1ccc2ncnc(N(C(=O)[C@]([O-])([SiH3])c3ccccc3)c3cccc(Br)c3)c2c1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 8, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 7, 7, 7, 3, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 23, 15, 6, 1, 6, 1, 1, 1, 2, 2, 1, 2, 2, 15, 42, 42, 42, 42, 42, 42, 23, 23, 23, 23, 23, 23, 23, 2, 2, 1, 2, 2, 42, 42, 42, 42, 23] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142688092 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142688092/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142688092 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 773) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/773: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1ccc2ncnc(N(C(=O)[C@@]([O-])([SiH3])c3ccccc3)c3cccc(Br)c3)c2c1) `ZINC001142688092.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142688092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142688092/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001142688092 none Nc1ccc2ncnc(N(C(=O)[C@@]([O-])([SiH3])c3ccccc3)c3cccc(Br)c3)c2c1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 8, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 7, 7, 7, 3, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 14, 6, 1, 6, 1, 1, 1, 2, 2, 1, 2, 2, 14, 42, 42, 32, 42, 42, 42, 22, 22, 22, 22, 22, 22, 22, 2, 2, 1, 2, 2, 42, 42, 39, 42, 22] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142688092 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001142688092 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142688092/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142688092/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142688092 Building ZINC001142693704 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142693704' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142693704 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142693704 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142693704/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142693704 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 774) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/774 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/774' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)c1cc2cccc(Cl)c2c(=O)n1c1ccccc1) `ZINC001142693704.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142693704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142693704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001142693704 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)c1cc2cccc(Cl)c2c(=O)n1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 11, 8, 1, 1, 1, 1, 1, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 13, 6, 1, 6, 1, 1, 1, 5, 5, 2, 5, 5, 13, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 45, 45, 45, 45, 45, 13, 13, 13, 6, 5, 5, 2, 5, 5, 39, 39, 39, 39, 45, 45, 45, 45, 45] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 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: 112 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142693704 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142693704/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142693704 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 775) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/775 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/775' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)c1cc2cccc(Cl)c2c(=O)n1c1ccccc1) `ZINC001142693704.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142693704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142693704/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001142693704 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)c1cc2cccc(Cl)c2c(=O)n1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 11, 8, 1, 1, 1, 1, 1, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 13, 6, 1, 6, 1, 1, 1, 5, 5, 1, 5, 5, 13, 40, 45, 45, 45, 41, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 13, 13, 13, 6, 5, 5, 1, 5, 5, 45, 40, 45, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 139 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142693704 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001142693704 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142693704/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142693704/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142693704 Building ZINC001142693704 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142693704' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142693704 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142693704 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142693704/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142693704 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 774) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/774: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)c1cc2cccc(Cl)c2c(=O)n1c1ccccc1) `ZINC001142693704.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142693704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142693704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001142693704 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)c1cc2cccc(Cl)c2c(=O)n1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 11, 8, 1, 1, 1, 1, 1, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 13, 6, 1, 6, 1, 1, 1, 5, 5, 2, 5, 5, 13, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 45, 45, 45, 45, 45, 13, 13, 13, 6, 5, 5, 2, 5, 5, 39, 39, 39, 39, 45, 45, 45, 45, 45] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 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: 112 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142693704 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142693704/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142693704 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 775) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/775: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)c1cc2cccc(Cl)c2c(=O)n1c1ccccc1) `ZINC001142693704.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142693704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142693704/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001142693704 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)c1cc2cccc(Cl)c2c(=O)n1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 11, 8, 1, 1, 1, 1, 1, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 13, 6, 1, 6, 1, 1, 1, 5, 5, 1, 5, 5, 13, 40, 45, 45, 45, 41, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 13, 13, 13, 6, 5, 5, 1, 5, 5, 45, 40, 45, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 139 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142693704 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001142693704 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142693704/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142693704/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142693704 Building ZINC001142695216 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142695216' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142695216 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142695216 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142695216/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142695216 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 776) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/776 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/776' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)Nc1ncnc2c1c(c1ccc(Oc3ccccc3)cc1)nn2C1CCCC1) `ZINC001142695216.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142695216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142695216/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001142695216 none C[C@@]([O-])([SiH3])C(=O)Nc1ncnc2c1c(c1ccc(Oc3ccccc3)cc1)nn2C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 13, 13, 10, 13, 32, 32, 32, 32, 32, 32, 13, 13, 7, 7, 7, 24, 24, 24, 24, 1, 1, 1, 3, 7, 13, 13, 32, 32, 32, 32, 32, 13, 13, 24, 24, 24, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [0, 1, 34, 35, 33, 2, 3] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142695216 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142695216/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142695216 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 777) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/777 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/777' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)Nc1ncnc2c1c(c1ccc(Oc3ccccc3)cc1)nn2C1CCCC1) `ZINC001142695216.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142695216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142695216/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001142695216 none C[C@]([O-])([SiH3])C(=O)Nc1ncnc2c1c(c1ccc(Oc3ccccc3)cc1)nn2C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 12, 12, 7, 10, 30, 30, 30, 30, 30, 30, 12, 12, 7, 7, 7, 24, 24, 24, 24, 1, 1, 1, 3, 7, 12, 12, 30, 30, 30, 30, 30, 12, 12, 24, 24, 24, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [0, 1, 34, 35, 33, 2, 3] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142695216 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001142695216 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142695216/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142695216/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142695216 Building ZINC001142695216 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142695216' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142695216 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142695216 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142695216/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142695216 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 776) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/776: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)Nc1ncnc2c1c(c1ccc(Oc3ccccc3)cc1)nn2C1CCCC1) `ZINC001142695216.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142695216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142695216/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001142695216 none C[C@@]([O-])([SiH3])C(=O)Nc1ncnc2c1c(c1ccc(Oc3ccccc3)cc1)nn2C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 13, 13, 10, 13, 32, 32, 32, 32, 32, 32, 13, 13, 7, 7, 7, 24, 24, 24, 24, 1, 1, 1, 3, 7, 13, 13, 32, 32, 32, 32, 32, 13, 13, 24, 24, 24, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [0, 1, 34, 35, 33, 2, 3] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142695216 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142695216/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142695216 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 777) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/777: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)Nc1ncnc2c1c(c1ccc(Oc3ccccc3)cc1)nn2C1CCCC1) `ZINC001142695216.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142695216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142695216/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001142695216 none C[C@]([O-])([SiH3])C(=O)Nc1ncnc2c1c(c1ccc(Oc3ccccc3)cc1)nn2C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 12, 12, 7, 10, 30, 30, 30, 30, 30, 30, 12, 12, 7, 7, 7, 24, 24, 24, 24, 1, 1, 1, 3, 7, 12, 12, 30, 30, 30, 30, 30, 12, 12, 24, 24, 24, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [0, 1, 34, 35, 33, 2, 3] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142695216 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001142695216 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142695216/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142695216/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142695216 Building ZINC001142695532 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142695532' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142695532 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142695532 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142695532/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142695532 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 778) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/778 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/778' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)c(NC(=O)Nc2ccc(c3cccc4[nH]nc(NC(=O)[C@@](C)([O-])[SiH3])c43)cc2)c1) `ZINC001142695532.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142695532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142695532/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 4 27 3 31 to be deleted 32 to be deleted 33 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001142695532 none Cc1ccc(F)c(NC(=O)Nc2ccc(c3cccc4[nH]nc(NC(=O)[C@@](C)([O-])[SiH3])c43)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 6, 8, 1, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 25, 21, 16, 21, 6, 6, 12, 12, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 6, 12, 12, 50, 50, 50, 50, 50, 50, 25, 16, 12, 12, 6, 6, 6, 3, 1, 1, 1, 12, 12, 50] 50 rigid atoms, others: [47, 48, 49, 25, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 50, 51, 52]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142695532 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142695532/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142695532 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 779) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/779 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/779' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)c(NC(=O)Nc2ccc(c3cccc4[nH]nc(NC(=O)[C@](C)([O-])[SiH3])c43)cc2)c1) `ZINC001142695532.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142695532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142695532/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 4 27 3 31 to be deleted 32 to be deleted 33 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001142695532 none Cc1ccc(F)c(NC(=O)Nc2ccc(c3cccc4[nH]nc(NC(=O)[C@](C)([O-])[SiH3])c43)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 6, 8, 1, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 23, 17, 23, 6, 6, 14, 14, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 6, 14, 14, 50, 50, 50, 50, 50, 50, 27, 17, 14, 14, 6, 6, 6, 3, 1, 1, 1, 14, 14, 50] 50 rigid atoms, others: [47, 48, 49, 25, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 50, 51, 52]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142695532 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001142695532 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142695532/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142695532/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142695532 Building ZINC001142695532 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142695532' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142695532 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142695532 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142695532/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142695532 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 778) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/778: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)c(NC(=O)Nc2ccc(c3cccc4[nH]nc(NC(=O)[C@@](C)([O-])[SiH3])c43)cc2)c1) `ZINC001142695532.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142695532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142695532/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 4 27 3 31 to be deleted 32 to be deleted 33 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001142695532 none Cc1ccc(F)c(NC(=O)Nc2ccc(c3cccc4[nH]nc(NC(=O)[C@@](C)([O-])[SiH3])c43)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 6, 8, 1, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 25, 21, 16, 21, 6, 6, 12, 12, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 6, 12, 12, 50, 50, 50, 50, 50, 50, 25, 16, 12, 12, 6, 6, 6, 3, 1, 1, 1, 12, 12, 50] 50 rigid atoms, others: [47, 48, 49, 25, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 50, 51, 52]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142695532 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142695532/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142695532 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 779) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/779: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)c(NC(=O)Nc2ccc(c3cccc4[nH]nc(NC(=O)[C@](C)([O-])[SiH3])c43)cc2)c1) `ZINC001142695532.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142695532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142695532/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 4 27 3 31 to be deleted 32 to be deleted 33 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001142695532 none Cc1ccc(F)c(NC(=O)Nc2ccc(c3cccc4[nH]nc(NC(=O)[C@](C)([O-])[SiH3])c43)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 6, 8, 1, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 23, 17, 23, 6, 6, 14, 14, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 6, 14, 14, 50, 50, 50, 50, 50, 50, 27, 17, 14, 14, 6, 6, 6, 3, 1, 1, 1, 14, 14, 50] 50 rigid atoms, others: [47, 48, 49, 25, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 50, 51, 52]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142695532 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001142695532 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142695532/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142695532/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142695532 Building ZINC001142699424 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699424' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699424 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142699424 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699424/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699424 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 780) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/780 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/780' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C(c2ccc(C)c(NC(=O)[C@@](C)([O-])[SiH3])c2)(C(F)(F)F)C(F)(F)F)cc1N) `ZINC001142699424.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142699424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 4 15 3 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001142699424 none Cc1ccc(C(c2ccc(C)c(NC(=O)[C@@](C)([O-])[SiH3])c2)(C(F)(F)F)C(F)(F)F)cc1N NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 1, 1, 1, 5, 1, 8, 1, 11, 5, 5, 12, 1, 5, 15, 15, 15, 5, 15, 15, 15, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 26, 5, 5, 3, 5, 5, 5, 3, 3, 1, 3, 1, 1, 1, 5, 26, 26, 26, 26, 26, 26, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 3, 5, 5, 5, 5, 3, 1, 1, 1, 5, 50, 50, 50] 50 rigid atoms, others: [41, 42, 43, 13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/129831/xbf-8058088.32/working/building/ZINC001142699424 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699424/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699424 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 781) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/781 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/781' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C(c2ccc(C)c(NC(=O)[C@](C)([O-])[SiH3])c2)(C(F)(F)F)C(F)(F)F)cc1N) `ZINC001142699424.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142699424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699424/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 4 15 3 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001142699424 none Cc1ccc(C(c2ccc(C)c(NC(=O)[C@](C)([O-])[SiH3])c2)(C(F)(F)F)C(F)(F)F)cc1N NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 1, 1, 1, 5, 1, 8, 1, 11, 5, 5, 12, 1, 5, 15, 15, 15, 5, 15, 15, 15, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 27, 6, 6, 3, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 6, 27, 27, 27, 27, 27, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 3, 6, 6, 6, 6, 3, 1, 1, 1, 6, 50, 50, 50] 50 rigid atoms, others: [41, 42, 43, 13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/129831/xbf-8058088.32/working/building/ZINC001142699424 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001142699424 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699424/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699424/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699424 Building ZINC001142699424 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699424' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699424 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142699424 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699424/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699424 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 780) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/780: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C(c2ccc(C)c(NC(=O)[C@@](C)([O-])[SiH3])c2)(C(F)(F)F)C(F)(F)F)cc1N) `ZINC001142699424.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142699424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 4 15 3 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001142699424 none Cc1ccc(C(c2ccc(C)c(NC(=O)[C@@](C)([O-])[SiH3])c2)(C(F)(F)F)C(F)(F)F)cc1N NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 1, 1, 1, 5, 1, 8, 1, 11, 5, 5, 12, 1, 5, 15, 15, 15, 5, 15, 15, 15, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 26, 5, 5, 3, 5, 5, 5, 3, 3, 1, 3, 1, 1, 1, 5, 26, 26, 26, 26, 26, 26, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 3, 5, 5, 5, 5, 3, 1, 1, 1, 5, 50, 50, 50] 50 rigid atoms, others: [41, 42, 43, 13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/129831/xbf-8058088.32/working/building/ZINC001142699424 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699424/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699424 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 781) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/781: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C(c2ccc(C)c(NC(=O)[C@](C)([O-])[SiH3])c2)(C(F)(F)F)C(F)(F)F)cc1N) `ZINC001142699424.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142699424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699424/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 4 15 3 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001142699424 none Cc1ccc(C(c2ccc(C)c(NC(=O)[C@](C)([O-])[SiH3])c2)(C(F)(F)F)C(F)(F)F)cc1N NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 1, 1, 1, 5, 1, 8, 1, 11, 5, 5, 12, 1, 5, 15, 15, 15, 5, 15, 15, 15, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 27, 6, 6, 3, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 6, 27, 27, 27, 27, 27, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 3, 6, 6, 6, 6, 3, 1, 1, 1, 6, 50, 50, 50] 50 rigid atoms, others: [41, 42, 43, 13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/129831/xbf-8058088.32/working/building/ZINC001142699424 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001142699424 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699424/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699424/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699424 Building ZINC001142699636 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142699636 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 782) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/782 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/782' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@](C)([O-])[SiH3])C1CCCCC1) `ZINC001142699636.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142699636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 4 14 3 18 to be deleted 19 to be deleted 20 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001142699636 none CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@](C)([O-])[SiH3])C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 17, 1, 1, 17, 1, 8, 1, 11, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 25, 19, 19, 19, 5, 11, 19, 19, 19, 5, 5, 1, 5, 1, 1, 1, 34, 50, 50, 50, 50, 50, 30, 30, 30, 25, 25, 19, 19, 5, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 12, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 168 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 783) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/783 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/783' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@@](C)([O-])[SiH3])C1CCCCC1) `ZINC001142699636.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142699636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 4 14 3 18 to be deleted 19 to be deleted 20 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001142699636 none CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@@](C)([O-])[SiH3])C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 17, 1, 1, 17, 1, 8, 1, 11, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 22, 17, 17, 17, 11, 13, 17, 17, 17, 5, 5, 1, 5, 1, 1, 1, 33, 50, 50, 50, 50, 50, 28, 28, 28, 22, 22, 17, 17, 5, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 12, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 155 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 784) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/784 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/784' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@](C)([O-])[SiH3])C1CCCCC1) `ZINC001142699636.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142699636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 4 14 3 18 to be deleted 19 to be deleted 20 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001142699636 none CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@](C)([O-])[SiH3])C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 17, 1, 1, 17, 1, 8, 1, 11, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 25, 19, 19, 19, 5, 11, 19, 19, 19, 5, 5, 1, 5, 1, 1, 1, 34, 50, 50, 50, 50, 50, 30, 30, 30, 25, 25, 19, 19, 5, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 12, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 168 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 785) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/785 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/785' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@@](C)([O-])[SiH3])C1CCCCC1) `ZINC001142699636.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142699636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 4 14 3 18 to be deleted 19 to be deleted 20 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001142699636 none CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@@](C)([O-])[SiH3])C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 17, 1, 1, 17, 1, 8, 1, 11, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 22, 17, 17, 17, 11, 13, 17, 17, 17, 5, 5, 1, 5, 1, 1, 1, 33, 50, 50, 50, 50, 50, 28, 28, 28, 22, 22, 17, 17, 5, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 12, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 155 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001142699636 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636 Building ZINC001142699636 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142699636 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 782) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/782: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@](C)([O-])[SiH3])C1CCCCC1) `ZINC001142699636.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142699636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 4 14 3 18 to be deleted 19 to be deleted 20 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001142699636 none CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@](C)([O-])[SiH3])C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 17, 1, 1, 17, 1, 8, 1, 11, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 25, 19, 19, 19, 5, 11, 19, 19, 19, 5, 5, 1, 5, 1, 1, 1, 34, 50, 50, 50, 50, 50, 30, 30, 30, 25, 25, 19, 19, 5, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 12, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 168 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 783) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/783: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@@](C)([O-])[SiH3])C1CCCCC1) `ZINC001142699636.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142699636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 4 14 3 18 to be deleted 19 to be deleted 20 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001142699636 none CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@@](C)([O-])[SiH3])C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 17, 1, 1, 17, 1, 8, 1, 11, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 22, 17, 17, 17, 11, 13, 17, 17, 17, 5, 5, 1, 5, 1, 1, 1, 33, 50, 50, 50, 50, 50, 28, 28, 28, 22, 22, 17, 17, 5, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 12, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 155 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 784) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/784: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@](C)([O-])[SiH3])C1CCCCC1) `ZINC001142699636.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142699636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 4 14 3 18 to be deleted 19 to be deleted 20 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001142699636 none CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@](C)([O-])[SiH3])C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 17, 1, 1, 17, 1, 8, 1, 11, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 25, 19, 19, 19, 5, 11, 19, 19, 19, 5, 5, 1, 5, 1, 1, 1, 34, 50, 50, 50, 50, 50, 30, 30, 30, 25, 25, 19, 19, 5, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 12, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 168 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 785) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/785: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@@](C)([O-])[SiH3])C1CCCCC1) `ZINC001142699636.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142699636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 4 14 3 18 to be deleted 19 to be deleted 20 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001142699636 none CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@@](C)([O-])[SiH3])C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 17, 1, 1, 17, 1, 8, 1, 11, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 22, 17, 17, 17, 11, 13, 17, 17, 17, 5, 5, 1, 5, 1, 1, 1, 33, 50, 50, 50, 50, 50, 28, 28, 28, 22, 22, 17, 17, 5, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 12, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 155 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001142699636 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636 Building ZINC001142699636 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142699636 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 782) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/782: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@](C)([O-])[SiH3])C1CCCCC1) `ZINC001142699636.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142699636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 4 14 3 18 to be deleted 19 to be deleted 20 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001142699636 none CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@](C)([O-])[SiH3])C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 17, 1, 1, 17, 1, 8, 1, 11, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 25, 19, 19, 19, 5, 11, 19, 19, 19, 5, 5, 1, 5, 1, 1, 1, 34, 50, 50, 50, 50, 50, 30, 30, 30, 25, 25, 19, 19, 5, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 12, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 168 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 783) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/783: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@@](C)([O-])[SiH3])C1CCCCC1) `ZINC001142699636.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142699636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 4 14 3 18 to be deleted 19 to be deleted 20 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001142699636 none CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@@](C)([O-])[SiH3])C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 17, 1, 1, 17, 1, 8, 1, 11, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 22, 17, 17, 17, 11, 13, 17, 17, 17, 5, 5, 1, 5, 1, 1, 1, 33, 50, 50, 50, 50, 50, 28, 28, 28, 22, 22, 17, 17, 5, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 12, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 155 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 784) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/784: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@](C)([O-])[SiH3])C1CCCCC1) `ZINC001142699636.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142699636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 4 14 3 18 to be deleted 19 to be deleted 20 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001142699636 none CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@](C)([O-])[SiH3])C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 17, 1, 1, 17, 1, 8, 1, 11, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 25, 19, 19, 19, 5, 11, 19, 19, 19, 5, 5, 1, 5, 1, 1, 1, 34, 50, 50, 50, 50, 50, 30, 30, 30, 25, 25, 19, 19, 5, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 12, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 168 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 785) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/785: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@@](C)([O-])[SiH3])C1CCCCC1) `ZINC001142699636.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142699636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 4 14 3 18 to be deleted 19 to be deleted 20 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001142699636 none CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@@](C)([O-])[SiH3])C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 17, 1, 1, 17, 1, 8, 1, 11, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 22, 17, 17, 17, 11, 13, 17, 17, 17, 5, 5, 1, 5, 1, 1, 1, 33, 50, 50, 50, 50, 50, 28, 28, 28, 22, 22, 17, 17, 5, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 12, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 155 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001142699636 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636 Building ZINC001142699636 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142699636 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 782) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/782: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@](C)([O-])[SiH3])C1CCCCC1) `ZINC001142699636.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142699636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 4 14 3 18 to be deleted 19 to be deleted 20 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001142699636 none CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@](C)([O-])[SiH3])C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 17, 1, 1, 17, 1, 8, 1, 11, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 25, 19, 19, 19, 5, 11, 19, 19, 19, 5, 5, 1, 5, 1, 1, 1, 34, 50, 50, 50, 50, 50, 30, 30, 30, 25, 25, 19, 19, 5, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 12, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 168 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 783) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/783: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@@](C)([O-])[SiH3])C1CCCCC1) `ZINC001142699636.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142699636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 4 14 3 18 to be deleted 19 to be deleted 20 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001142699636 none CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@@](C)([O-])[SiH3])C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 17, 1, 1, 17, 1, 8, 1, 11, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 22, 17, 17, 17, 11, 13, 17, 17, 17, 5, 5, 1, 5, 1, 1, 1, 33, 50, 50, 50, 50, 50, 28, 28, 28, 22, 22, 17, 17, 5, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 12, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 155 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 784) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/784: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@](C)([O-])[SiH3])C1CCCCC1) `ZINC001142699636.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142699636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 4 14 3 18 to be deleted 19 to be deleted 20 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001142699636 none CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@](C)([O-])[SiH3])C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 17, 1, 1, 17, 1, 8, 1, 11, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 25, 19, 19, 19, 5, 11, 19, 19, 19, 5, 5, 1, 5, 1, 1, 1, 34, 50, 50, 50, 50, 50, 30, 30, 30, 25, 25, 19, 19, 5, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 12, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 168 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 785) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/785: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@@](C)([O-])[SiH3])C1CCCCC1) `ZINC001142699636.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142699636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 4 14 3 18 to be deleted 19 to be deleted 20 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001142699636 none CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@@](C)([O-])[SiH3])C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 17, 1, 1, 17, 1, 8, 1, 11, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 22, 17, 17, 17, 11, 13, 17, 17, 17, 5, 5, 1, 5, 1, 1, 1, 33, 50, 50, 50, 50, 50, 28, 28, 28, 22, 22, 17, 17, 5, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 12, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 155 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001142699636 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699636 Building ZINC001142699725 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699725' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699725 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142699725 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699725/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699725 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 786) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/786 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/786' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(CN3CCCC3)nn(Cc3c(Cl)cccc3Cl)c2c1) `ZINC001142699725.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142699725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001142699725 none C[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(CN3CCCC3)nn(Cc3c(Cl)cccc3Cl)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 5, 8, 8, 5, 1, 1, 16, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 17, 17, 17, 17, 17, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 1, 1, 1, 1, 4, 4, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 12, 12, 12, 12, 12, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 33, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699725 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699725/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699725 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 787) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/787 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/787' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)Nc1ccc2c(CN3CCCC3)nn(Cc3c(Cl)cccc3Cl)c2c1) `ZINC001142699725.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142699725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699725/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001142699725 none C[C@]([O-])([SiH3])C(=O)Nc1ccc2c(CN3CCCC3)nn(Cc3c(Cl)cccc3Cl)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 5, 8, 8, 5, 1, 1, 16, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 17, 17, 17, 17, 17, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 1, 1, 1, 1, 4, 4, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 12, 12, 12, 12, 12, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 33, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699725 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001142699725 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699725/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699725/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699725 Building ZINC001142699725 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699725' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699725 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142699725 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699725/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699725 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 786) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/786: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(CN3CCCC3)nn(Cc3c(Cl)cccc3Cl)c2c1) `ZINC001142699725.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142699725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001142699725 none C[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(CN3CCCC3)nn(Cc3c(Cl)cccc3Cl)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 5, 8, 8, 5, 1, 1, 16, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 17, 17, 17, 17, 17, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 1, 1, 1, 1, 4, 4, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 12, 12, 12, 12, 12, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 33, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699725 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699725/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699725 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 787) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/787: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)Nc1ccc2c(CN3CCCC3)nn(Cc3c(Cl)cccc3Cl)c2c1) `ZINC001142699725.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142699725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699725/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001142699725 none C[C@]([O-])([SiH3])C(=O)Nc1ccc2c(CN3CCCC3)nn(Cc3c(Cl)cccc3Cl)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 5, 8, 8, 5, 1, 1, 16, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 17, 17, 17, 17, 17, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 1, 1, 1, 1, 4, 4, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 12, 12, 12, 12, 12, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 33, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699725 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001142699725 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699725/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699725/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001142699725 Building ZINC001150945490 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001150945490' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001150945490 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001150945490 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001150945490/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001150945490 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 788) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/788 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/788' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@H](c1c[nH]c2ccccc21)c1ccc(Cl)cc1Cl) `ZINC001150945490.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001150945490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001150945490/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001150945490 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@H](c1c[nH]c2ccccc21)c1ccc(Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 16, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 17, 30, 30, 48, 48, 48, 48, 48, 48, 48, 48, 48, 30, 44, 44, 30, 30, 44, 44, 44, 4, 4, 4, 4, 4, 4, 3, 17, 17, 48, 48, 48, 48, 48, 44, 44, 44] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001150945490 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001150945490/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001150945490 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 789) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/789 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/789' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@H](c1c[nH]c2ccccc21)c1ccc(Cl)cc1Cl) `ZINC001150945490.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001150945490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001150945490/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001150945490 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@H](c1c[nH]c2ccccc21)c1ccc(Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 16, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 16, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 45, 45, 34, 34, 45, 45, 45, 3, 3, 3, 3, 3, 3, 3, 16, 16, 50, 50, 50, 50, 50, 45, 45, 45] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001150945490 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001150945490 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001150945490/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001150945490/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001150945490 Building ZINC001150945490 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001150945490' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001150945490 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001150945490 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001150945490/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001150945490 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 788) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/788: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@H](c1c[nH]c2ccccc21)c1ccc(Cl)cc1Cl) `ZINC001150945490.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001150945490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001150945490/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001150945490 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@H](c1c[nH]c2ccccc21)c1ccc(Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 16, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 17, 30, 30, 48, 48, 48, 48, 48, 48, 48, 48, 48, 30, 44, 44, 30, 30, 44, 44, 44, 4, 4, 4, 4, 4, 4, 3, 17, 17, 48, 48, 48, 48, 48, 44, 44, 44] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001150945490 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001150945490/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001150945490 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 789) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/789: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@H](c1c[nH]c2ccccc21)c1ccc(Cl)cc1Cl) `ZINC001150945490.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001150945490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001150945490/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001150945490 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@H](c1c[nH]c2ccccc21)c1ccc(Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 16, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 16, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 45, 45, 34, 34, 45, 45, 45, 3, 3, 3, 3, 3, 3, 3, 16, 16, 50, 50, 50, 50, 50, 45, 45, 45] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001150945490 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001150945490 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001150945490/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001150945490/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001150945490 Building ZINC001150945491 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001150945491' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001150945491 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001150945491 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001150945491/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001150945491 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 790) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/790 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/790' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1c[nH]c2ccccc21)c1ccc(Cl)cc1Cl) `ZINC001150945491.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001150945491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001150945491/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001150945491 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1c[nH]c2ccccc21)c1ccc(Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 16, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 16, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 45, 45, 34, 34, 45, 45, 45, 3, 3, 3, 3, 3, 3, 3, 16, 16, 50, 50, 50, 50, 50, 45, 45, 45] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001150945491 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001150945491/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001150945491 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 791) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/791 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/791' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@@H](c1c[nH]c2ccccc21)c1ccc(Cl)cc1Cl) `ZINC001150945491.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001150945491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001150945491/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001150945491 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@@H](c1c[nH]c2ccccc21)c1ccc(Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 16, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 17, 31, 31, 49, 49, 49, 49, 49, 49, 49, 49, 49, 31, 45, 45, 31, 31, 45, 45, 45, 3, 3, 3, 3, 3, 3, 3, 17, 17, 49, 49, 49, 49, 49, 45, 45, 45] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001150945491 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001150945491 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001150945491/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001150945491/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001150945491 Building ZINC001150945491 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001150945491' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001150945491 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001150945491 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001150945491/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001150945491 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 790) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/790: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1c[nH]c2ccccc21)c1ccc(Cl)cc1Cl) `ZINC001150945491.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001150945491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001150945491/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001150945491 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1c[nH]c2ccccc21)c1ccc(Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 16, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 16, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 45, 45, 34, 34, 45, 45, 45, 3, 3, 3, 3, 3, 3, 3, 16, 16, 50, 50, 50, 50, 50, 45, 45, 45] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001150945491 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001150945491/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001150945491 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 791) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/791: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@@H](c1c[nH]c2ccccc21)c1ccc(Cl)cc1Cl) `ZINC001150945491.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001150945491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001150945491/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001150945491 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@@H](c1c[nH]c2ccccc21)c1ccc(Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 16, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 17, 31, 31, 49, 49, 49, 49, 49, 49, 49, 49, 49, 31, 45, 45, 31, 31, 45, 45, 45, 3, 3, 3, 3, 3, 3, 3, 17, 17, 49, 49, 49, 49, 49, 45, 45, 45] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001150945491 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001150945491 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001150945491/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001150945491/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001150945491 Building ZINC001151395790 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001151395790' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001151395790 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001151395790 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001151395790/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001151395790 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 792) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/792 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/792' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2cccc(Br)c2)CCCC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001151395790.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001151395790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001151395790/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001151395790 none O=C(NCC1(c2cccc(Br)c2)CCCC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 15, 19, 33, 33, 33, 33, 33, 33, 19, 19, 19, 19, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 14, 14, 33, 33, 33, 33, 19, 19, 19, 19, 19, 19, 19, 19, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001151395790 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001151395790/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001151395790 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 793) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/793 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/793' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2cccc(Br)c2)CCCC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001151395790.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001151395790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001151395790/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001151395790 none O=C(NCC1(c2cccc(Br)c2)CCCC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 18, 23, 33, 33, 33, 33, 33, 33, 23, 23, 23, 23, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 12, 12, 33, 33, 33, 33, 23, 23, 23, 23, 23, 23, 23, 23, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 87 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001151395790 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001151395790 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001151395790/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001151395790/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001151395790 Building ZINC001151395790 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001151395790' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001151395790 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001151395790 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001151395790/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001151395790 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 792) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/792: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2cccc(Br)c2)CCCC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001151395790.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001151395790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001151395790/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001151395790 none O=C(NCC1(c2cccc(Br)c2)CCCC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 15, 19, 33, 33, 33, 33, 33, 33, 19, 19, 19, 19, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 14, 14, 33, 33, 33, 33, 19, 19, 19, 19, 19, 19, 19, 19, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001151395790 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001151395790/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001151395790 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 793) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/793: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2cccc(Br)c2)CCCC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001151395790.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001151395790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001151395790/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001151395790 none O=C(NCC1(c2cccc(Br)c2)CCCC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 18, 23, 33, 33, 33, 33, 33, 33, 23, 23, 23, 23, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 12, 12, 33, 33, 33, 33, 23, 23, 23, 23, 23, 23, 23, 23, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 87 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001151395790 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001151395790 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001151395790/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001151395790/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001151395790 Building ZINC001151812473 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001151812473' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001151812473 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001151812473 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001151812473/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001151812473 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 794) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/794 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/794' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C1C[C@H]2CC[C@@H](C1)N2C(=O)OC(C)(C)C) `ZINC001151812473.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001151812473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001151812473/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001151812473 none CN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C1C[C@H]2CC[C@@H](C1)N2C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 29, 29, 50, 50, 50, 50, 7, 7, 7, 3, 1, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 129 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001151812473 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001151812473/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001151812473 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 795) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/795 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/795' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C1C[C@H]2CC[C@@H](C1)N2C(=O)OC(C)(C)C) `ZINC001151812473.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001151812473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001151812473/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001151812473 none CN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C1C[C@H]2CC[C@@H](C1)N2C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 32, 32, 49, 49, 49, 49, 6, 6, 6, 3, 1, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 49, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 129 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001151812473 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001151812473 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001151812473/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001151812473/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001151812473 Building ZINC001151812473 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001151812473' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001151812473 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001151812473 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001151812473/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001151812473 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 794) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/794: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C1C[C@H]2CC[C@@H](C1)N2C(=O)OC(C)(C)C) `ZINC001151812473.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001151812473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001151812473/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001151812473 none CN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C1C[C@H]2CC[C@@H](C1)N2C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 29, 29, 50, 50, 50, 50, 7, 7, 7, 3, 1, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 129 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001151812473 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001151812473/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001151812473 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 795) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/795: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C1C[C@H]2CC[C@@H](C1)N2C(=O)OC(C)(C)C) `ZINC001151812473.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001151812473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001151812473/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001151812473 none CN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C1C[C@H]2CC[C@@H](C1)N2C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 32, 32, 49, 49, 49, 49, 6, 6, 6, 3, 1, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 49, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 129 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001151812473 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001151812473 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001151812473/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001151812473/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001151812473 Building ZINC001152303131 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001152303131' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001152303131 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001152303131 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001152303131/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001152303131 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 796) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/796 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/796' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCc1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cnn1c1cccc(F)c1) `ZINC001152303131.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001152303131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001152303131/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001152303131 none CCCc1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cnn1c1cccc(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 7, 7, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 7, 7, 7, 7, 27, 27, 27, 27, 27, 27, 14, 14, 14, 14, 14, 14, 14, 3, 8, 8, 7, 27, 27, 27, 27] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001152303131 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001152303131/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001152303131 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 797) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/797 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/797' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCc1c(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cnn1c1cccc(F)c1) `ZINC001152303131.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001152303131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001152303131/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001152303131 none CCCc1c(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cnn1c1cccc(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 7, 7, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 7, 7, 7, 7, 28, 28, 28, 28, 28, 28, 14, 14, 14, 14, 14, 14, 14, 3, 8, 8, 7, 28, 28, 28, 28] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001152303131 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001152303131 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001152303131/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001152303131/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001152303131 Building ZINC001152303131 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001152303131' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001152303131 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001152303131 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001152303131/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001152303131 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 796) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/796: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCc1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cnn1c1cccc(F)c1) `ZINC001152303131.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001152303131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001152303131/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001152303131 none CCCc1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cnn1c1cccc(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 7, 7, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 7, 7, 7, 7, 27, 27, 27, 27, 27, 27, 14, 14, 14, 14, 14, 14, 14, 3, 8, 8, 7, 27, 27, 27, 27] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001152303131 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001152303131/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001152303131 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 797) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/797: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCc1c(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cnn1c1cccc(F)c1) `ZINC001152303131.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001152303131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001152303131/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001152303131 none CCCc1c(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cnn1c1cccc(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 7, 7, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 7, 7, 7, 7, 28, 28, 28, 28, 28, 28, 14, 14, 14, 14, 14, 14, 14, 3, 8, 8, 7, 28, 28, 28, 28] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001152303131 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001152303131 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001152303131/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001152303131/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001152303131 Building ZINC001153505202 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153505202' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153505202 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001153505202 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153505202/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153505202 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 798) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/798 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/798' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(Cc1ccccc1)C[C@@H](O)c1cccc(OCc2ccccc2)c1) `ZINC001153505202.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001153505202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153505202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001153505202 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(Cc1ccccc1)C[C@@H](O)c1cccc(OCc2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of 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, 4, 4, 3, 4, 4, 2, 3, 4, 4, 4, 13, 13, 13, 13, 13, 24, 28, 43, 43, 35, 43, 43, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 3, 4, 4, 3, 3, 12, 13, 13, 13, 28, 28, 43, 43, 43, 43, 43, 13] 150 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 39, 40, 41, 42, 2, 3, 4, 6, 5] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 166 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153505202 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153505202/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153505202 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 799) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/799 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/799' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N(Cc1ccccc1)C[C@@H](O)c1cccc(OCc2ccccc2)c1) `ZINC001153505202.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001153505202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153505202/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001153505202 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N(Cc1ccccc1)C[C@@H](O)c1cccc(OCc2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 6, 3, 5, 8, 8, 8, 25, 25, 25, 25, 25, 42, 42, 45, 45, 43, 45, 45, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 5, 5, 24, 25, 25, 25, 42, 42, 45, 45, 45, 45, 45, 25] 150 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 39, 40, 41, 42, 2, 3, 4, 6, 5] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 147 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153505202 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001153505202 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153505202/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153505202/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153505202 Building ZINC001153505202 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153505202' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153505202 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001153505202 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153505202/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153505202 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 798) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/798: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(Cc1ccccc1)C[C@@H](O)c1cccc(OCc2ccccc2)c1) `ZINC001153505202.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001153505202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153505202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001153505202 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(Cc1ccccc1)C[C@@H](O)c1cccc(OCc2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of 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, 4, 4, 3, 4, 4, 2, 3, 4, 4, 4, 13, 13, 13, 13, 13, 24, 28, 43, 43, 35, 43, 43, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 3, 4, 4, 3, 3, 12, 13, 13, 13, 28, 28, 43, 43, 43, 43, 43, 13] 150 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 39, 40, 41, 42, 2, 3, 4, 6, 5] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 166 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153505202 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153505202/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153505202 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 799) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/799: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N(Cc1ccccc1)C[C@@H](O)c1cccc(OCc2ccccc2)c1) `ZINC001153505202.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001153505202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153505202/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001153505202 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N(Cc1ccccc1)C[C@@H](O)c1cccc(OCc2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 6, 3, 5, 8, 8, 8, 25, 25, 25, 25, 25, 42, 42, 45, 45, 43, 45, 45, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 5, 5, 24, 25, 25, 25, 42, 42, 45, 45, 45, 45, 45, 25] 150 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 39, 40, 41, 42, 2, 3, 4, 6, 5] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 147 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153505202 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001153505202 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153505202/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153505202/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153505202 Building ZINC001153505204 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153505204' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153505204 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001153505204 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153505204/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153505204 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 800) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/800 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/800' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(Cc1ccccc1)C[C@H](O)c1cccc(OCc2ccccc2)c1) `ZINC001153505204.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001153505204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153505204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001153505204 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(Cc1ccccc1)C[C@H](O)c1cccc(OCc2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 2, 4, 8, 8, 8, 26, 26, 26, 26, 26, 36, 36, 42, 42, 39, 42, 42, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 4, 4, 24, 26, 26, 26, 36, 36, 42, 42, 42, 42, 42, 26] 150 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 39, 40, 41, 42, 2, 3, 4, 6, 5] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 150 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153505204 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153505204/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153505204 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 801) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/801 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/801' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N(Cc1ccccc1)C[C@H](O)c1cccc(OCc2ccccc2)c1) `ZINC001153505204.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001153505204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153505204/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001153505204 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N(Cc1ccccc1)C[C@H](O)c1cccc(OCc2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of 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, 4, 4, 3, 4, 4, 2, 3, 4, 4, 4, 14, 14, 14, 14, 14, 25, 30, 45, 45, 34, 45, 45, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 3, 3, 12, 14, 14, 14, 30, 30, 45, 45, 45, 45, 45, 14] 150 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 39, 40, 41, 42, 2, 3, 4, 6, 5] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 183 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153505204 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001153505204 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153505204/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153505204/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153505204 Building ZINC001153505204 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153505204' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153505204 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001153505204 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153505204/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153505204 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 800) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/800: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(Cc1ccccc1)C[C@H](O)c1cccc(OCc2ccccc2)c1) `ZINC001153505204.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001153505204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153505204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001153505204 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(Cc1ccccc1)C[C@H](O)c1cccc(OCc2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 2, 4, 8, 8, 8, 26, 26, 26, 26, 26, 36, 36, 42, 42, 39, 42, 42, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 4, 4, 24, 26, 26, 26, 36, 36, 42, 42, 42, 42, 42, 26] 150 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 39, 40, 41, 42, 2, 3, 4, 6, 5] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 150 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153505204 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153505204/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153505204 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 801) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/801: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N(Cc1ccccc1)C[C@H](O)c1cccc(OCc2ccccc2)c1) `ZINC001153505204.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001153505204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153505204/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001153505204 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N(Cc1ccccc1)C[C@H](O)c1cccc(OCc2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of 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, 4, 4, 3, 4, 4, 2, 3, 4, 4, 4, 14, 14, 14, 14, 14, 25, 30, 45, 45, 34, 45, 45, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 3, 3, 12, 14, 14, 14, 30, 30, 45, 45, 45, 45, 45, 14] 150 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 39, 40, 41, 42, 2, 3, 4, 6, 5] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 183 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153505204 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001153505204 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153505204/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153505204/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153505204 Building ZINC001153982004 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153982004' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153982004 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001153982004 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153982004/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153982004 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 802) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/802 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/802' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1cc(F)cc(CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1) `ZINC001153982004.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001153982004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153982004/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001153982004 none CC(C)(C)OC(=O)Nc1cc(F)cc(CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.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, 12, 1, 11, 8, 1, 1, 1, 15, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 33, 50, 17, 17, 17, 17, 17, 17, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 17, 17, 7, 7, 1, 1, 1, 1, 17] 50 rigid atoms, others: [43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153982004 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153982004/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153982004 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 803) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/803 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/803' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1cc(F)cc(CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1) `ZINC001153982004.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001153982004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153982004/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001153982004 none CC(C)(C)OC(=O)Nc1cc(F)cc(CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.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, 12, 1, 11, 8, 1, 1, 1, 15, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 34, 50, 17, 17, 17, 17, 17, 17, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 17, 17, 7, 7, 1, 1, 1, 1, 17] 50 rigid atoms, others: [43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 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/129831/xbf-8058088.32/working/building/ZINC001153982004 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001153982004 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153982004/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153982004/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153982004 Building ZINC001153982004 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153982004' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153982004 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001153982004 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153982004/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153982004 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 802) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/802: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1cc(F)cc(CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1) `ZINC001153982004.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001153982004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153982004/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001153982004 none CC(C)(C)OC(=O)Nc1cc(F)cc(CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.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, 12, 1, 11, 8, 1, 1, 1, 15, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 33, 50, 17, 17, 17, 17, 17, 17, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 17, 17, 7, 7, 1, 1, 1, 1, 17] 50 rigid atoms, others: [43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153982004 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153982004/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153982004 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 803) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/803: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1cc(F)cc(CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1) `ZINC001153982004.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001153982004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153982004/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001153982004 none CC(C)(C)OC(=O)Nc1cc(F)cc(CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.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, 12, 1, 11, 8, 1, 1, 1, 15, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 34, 50, 17, 17, 17, 17, 17, 17, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 17, 17, 7, 7, 1, 1, 1, 1, 17] 50 rigid atoms, others: [43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 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/129831/xbf-8058088.32/working/building/ZINC001153982004 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001153982004 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153982004/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153982004/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001153982004 Building ZINC001154245865 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154245865' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154245865 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001154245865 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154245865/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154245865 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 804) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/804 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/804' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCc1c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1ccc(C)cc1) `ZINC001154245865.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001154245865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154245865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001154245865 none CCCc1c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 17, 17, 17, 17, 17, 9, 9, 2, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 4, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 95 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154245865 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154245865/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154245865 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 805) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/805 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/805' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCc1c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1ccc(C)cc1) `ZINC001154245865.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001154245865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154245865/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001154245865 none CCCc1c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 7, 7, 4, 7, 7, 4, 4, 5, 5, 5, 5, 11, 11, 5, 10, 11, 11, 15, 15, 15, 15, 15, 10, 10, 2, 4, 4, 4, 7, 7, 4, 7, 7, 4, 4, 4, 5, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 132 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154245865 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001154245865 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154245865/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154245865/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154245865 Building ZINC001154245865 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154245865' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154245865 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001154245865 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154245865/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154245865 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 804) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/804: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCc1c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1ccc(C)cc1) `ZINC001154245865.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001154245865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154245865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001154245865 none CCCc1c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 17, 17, 17, 17, 17, 9, 9, 2, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 4, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 95 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154245865 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154245865/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154245865 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 805) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/805: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCc1c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1ccc(C)cc1) `ZINC001154245865.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001154245865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154245865/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001154245865 none CCCc1c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 7, 7, 4, 7, 7, 4, 4, 5, 5, 5, 5, 11, 11, 5, 10, 11, 11, 15, 15, 15, 15, 15, 10, 10, 2, 4, 4, 4, 7, 7, 4, 7, 7, 4, 4, 4, 5, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 132 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154245865 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001154245865 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154245865/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154245865/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154245865 Building ZINC001154423761 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154423761' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154423761 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001154423761 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154423761/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154423761 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 806) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/806 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/806' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCCCC1)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1O) `ZINC001154423761.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001154423761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154423761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001154423761 none O=C(NC1CCCCC1)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [15, 9, 15, 28, 50, 50, 50, 50, 50, 9, 9, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 9, 9, 9, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 2, 2, 1, 2, 9, 18] 100 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 175 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154423761 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154423761/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154423761 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 807) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/807 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/807' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCCCC1)c1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1O) `ZINC001154423761.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001154423761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154423761/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001154423761 none O=C(NC1CCCCC1)c1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [15, 9, 15, 28, 50, 50, 50, 50, 50, 9, 9, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 9, 9, 9, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 2, 2, 1, 2, 9, 18] 100 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 175 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154423761 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001154423761 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154423761/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154423761/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154423761 Building ZINC001154423761 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154423761' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154423761 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001154423761 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154423761/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154423761 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 806) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/806: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCCCC1)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1O) `ZINC001154423761.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001154423761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154423761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001154423761 none O=C(NC1CCCCC1)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [15, 9, 15, 28, 50, 50, 50, 50, 50, 9, 9, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 9, 9, 9, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 2, 2, 1, 2, 9, 18] 100 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 175 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154423761 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154423761/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154423761 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 807) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/807: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCCCC1)c1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1O) `ZINC001154423761.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001154423761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154423761/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001154423761 none O=C(NC1CCCCC1)c1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [15, 9, 15, 28, 50, 50, 50, 50, 50, 9, 9, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 9, 9, 9, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 2, 2, 1, 2, 9, 18] 100 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 175 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154423761 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001154423761 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154423761/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154423761/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154423761 Building ZINC001154486652 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486652' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486652 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001154486652 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486652/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486652 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 808) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/808 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/808' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1[C@H](CNC(=O)OC(C)(C)C)Cc1ccccc1) `ZINC001154486652.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001154486652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 75 natoms 74 natoms 73 natoms 72 names: ZINC001154486652 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1[C@H](CNC(=O)OC(C)(C)C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', '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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 11, 17, 17, 19, 19, 19, 19, 3, 5, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 2, 5, 6, 7, 8, 9, 10, 11, 12, 45, 14, 47, 48, 49, 50, 51, 52, 46, 15, 13] set([0, 1, 3, 4, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71]) total number of confs: 85 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486652 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486652/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486652 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 809) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/809 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/809' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1[C@H](CNC(=O)OC(C)(C)C)Cc1ccccc1) `ZINC001154486652.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001154486652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486652/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 75 natoms 74 natoms 73 natoms 72 names: ZINC001154486652 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1[C@H](CNC(=O)OC(C)(C)C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', '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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 10, 13, 13, 20, 20, 20, 20, 2, 4, 4, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 2, 5, 6, 7, 8, 9, 10, 11, 12, 45, 14, 47, 48, 49, 50, 51, 52, 46, 15, 13] set([0, 1, 3, 4, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71]) total number of confs: 77 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486652 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001154486652 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486652/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486652/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486652 Building ZINC001154486652 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486652' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486652 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001154486652 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486652/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486652 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 808) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/808: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1[C@H](CNC(=O)OC(C)(C)C)Cc1ccccc1) `ZINC001154486652.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001154486652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 75 natoms 74 natoms 73 natoms 72 names: ZINC001154486652 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1[C@H](CNC(=O)OC(C)(C)C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', '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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 11, 17, 17, 19, 19, 19, 19, 3, 5, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 2, 5, 6, 7, 8, 9, 10, 11, 12, 45, 14, 47, 48, 49, 50, 51, 52, 46, 15, 13] set([0, 1, 3, 4, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71]) total number of confs: 85 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486652 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486652/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486652 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 809) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/809: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1[C@H](CNC(=O)OC(C)(C)C)Cc1ccccc1) `ZINC001154486652.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001154486652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486652/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 75 natoms 74 natoms 73 natoms 72 names: ZINC001154486652 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1[C@H](CNC(=O)OC(C)(C)C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', '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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 10, 13, 13, 20, 20, 20, 20, 2, 4, 4, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 2, 5, 6, 7, 8, 9, 10, 11, 12, 45, 14, 47, 48, 49, 50, 51, 52, 46, 15, 13] set([0, 1, 3, 4, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71]) total number of confs: 77 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486652 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001154486652 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486652/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486652/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486652 Building ZINC001154486653 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486653' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486653 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001154486653 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486653/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486653 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 810) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/810 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/810' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1[C@@H](CNC(=O)OC(C)(C)C)Cc1ccccc1) `ZINC001154486653.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001154486653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 75 natoms 74 natoms 73 natoms 72 names: ZINC001154486653 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1[C@@H](CNC(=O)OC(C)(C)C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', '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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 12, 17, 17, 19, 19, 19, 19, 3, 5, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 2, 5, 6, 7, 8, 9, 10, 11, 12, 45, 14, 47, 48, 49, 50, 51, 52, 46, 15, 13] set([0, 1, 3, 4, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71]) total number of confs: 90 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486653 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486653/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486653 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 811) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/811 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/811' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1[C@@H](CNC(=O)OC(C)(C)C)Cc1ccccc1) `ZINC001154486653.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001154486653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486653/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 75 natoms 74 natoms 73 natoms 72 names: ZINC001154486653 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1[C@@H](CNC(=O)OC(C)(C)C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', '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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 8, 13, 13, 17, 17, 17, 17, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [16, 2, 5, 6, 7, 8, 9, 10, 11, 12, 45, 14, 47, 48, 49, 50, 51, 52, 46, 15, 13] set([0, 1, 3, 4, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71]) total number of confs: 75 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486653 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001154486653 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486653/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486653/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486653 Building ZINC001154486653 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486653' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486653 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001154486653 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486653/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486653 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 810) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/810: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1[C@@H](CNC(=O)OC(C)(C)C)Cc1ccccc1) `ZINC001154486653.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001154486653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 75 natoms 74 natoms 73 natoms 72 names: ZINC001154486653 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1[C@@H](CNC(=O)OC(C)(C)C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', '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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 12, 17, 17, 19, 19, 19, 19, 3, 5, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 2, 5, 6, 7, 8, 9, 10, 11, 12, 45, 14, 47, 48, 49, 50, 51, 52, 46, 15, 13] set([0, 1, 3, 4, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71]) total number of confs: 90 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486653 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486653/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486653 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 811) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/811: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1[C@@H](CNC(=O)OC(C)(C)C)Cc1ccccc1) `ZINC001154486653.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001154486653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486653/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 75 natoms 74 natoms 73 natoms 72 names: ZINC001154486653 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1[C@@H](CNC(=O)OC(C)(C)C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', '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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 8, 13, 13, 17, 17, 17, 17, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [16, 2, 5, 6, 7, 8, 9, 10, 11, 12, 45, 14, 47, 48, 49, 50, 51, 52, 46, 15, 13] set([0, 1, 3, 4, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71]) total number of confs: 75 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486653 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001154486653 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486653/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486653/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486653 Building ZINC001154486654 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486654' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486654 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001154486654 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486654/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486654 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 812) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/812 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/812' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCC[C@H]1[C@@H](CNC(=O)OC(C)(C)C)Cc1ccccc1) `ZINC001154486654.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001154486654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486654/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 75 natoms 74 natoms 73 natoms 72 names: ZINC001154486654 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCC[C@H]1[C@@H](CNC(=O)OC(C)(C)C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', '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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 8, 11, 11, 19, 20, 20, 20, 2, 4, 4, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 20, 20, 20, 20, 20, 20, 20, 20, 20, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 2, 5, 6, 7, 8, 9, 10, 11, 12, 45, 14, 47, 48, 49, 50, 51, 52, 46, 15, 13] set([0, 1, 3, 4, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71]) total number of confs: 80 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486654 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486654/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486654 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 813) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/813 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/813' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCC[C@H]1[C@@H](CNC(=O)OC(C)(C)C)Cc1ccccc1) `ZINC001154486654.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001154486654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486654/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 75 natoms 74 natoms 73 natoms 72 names: ZINC001154486654 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCC[C@H]1[C@@H](CNC(=O)OC(C)(C)C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', '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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 4, 4, 6, 11, 17, 17, 19, 19, 19, 19, 4, 6, 6, 6, 6, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [2, 5, 6, 7, 8, 9] set([0, 1, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71]) total number of confs: 85 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486654 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001154486654 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486654/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486654/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486654 Building ZINC001154486654 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486654' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486654 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001154486654 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486654/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486654 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 812) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/812: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCC[C@H]1[C@@H](CNC(=O)OC(C)(C)C)Cc1ccccc1) `ZINC001154486654.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001154486654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486654/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 75 natoms 74 natoms 73 natoms 72 names: ZINC001154486654 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCC[C@H]1[C@@H](CNC(=O)OC(C)(C)C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', '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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 8, 11, 11, 19, 20, 20, 20, 2, 4, 4, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 20, 20, 20, 20, 20, 20, 20, 20, 20, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 2, 5, 6, 7, 8, 9, 10, 11, 12, 45, 14, 47, 48, 49, 50, 51, 52, 46, 15, 13] set([0, 1, 3, 4, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71]) total number of confs: 80 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486654 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486654/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486654 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 813) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/813: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCC[C@H]1[C@@H](CNC(=O)OC(C)(C)C)Cc1ccccc1) `ZINC001154486654.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001154486654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486654/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 75 natoms 74 natoms 73 natoms 72 names: ZINC001154486654 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCC[C@H]1[C@@H](CNC(=O)OC(C)(C)C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', '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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 4, 4, 6, 11, 17, 17, 19, 19, 19, 19, 4, 6, 6, 6, 6, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [2, 5, 6, 7, 8, 9] set([0, 1, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71]) total number of confs: 85 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486654 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001154486654 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486654/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486654/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486654 Building ZINC001154486655 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486655' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486655 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001154486655 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486655/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486655 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 814) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/814 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/814' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCC[C@H]1[C@H](CNC(=O)OC(C)(C)C)Cc1ccccc1) `ZINC001154486655.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001154486655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486655/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 75 natoms 74 natoms 73 natoms 72 names: ZINC001154486655 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCC[C@H]1[C@H](CNC(=O)OC(C)(C)C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', '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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 9, 15, 15, 17, 17, 17, 17, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [16, 2, 5, 6, 7, 8, 9, 10, 11, 12, 45, 14, 47, 48, 49, 50, 51, 52, 46, 15, 13] set([0, 1, 3, 4, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71]) total number of confs: 74 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486655 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486655/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486655 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 815) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/815 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/815' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCC[C@H]1[C@H](CNC(=O)OC(C)(C)C)Cc1ccccc1) `ZINC001154486655.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001154486655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486655/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 75 natoms 74 natoms 73 natoms 72 names: ZINC001154486655 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCC[C@H]1[C@H](CNC(=O)OC(C)(C)C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', '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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 10, 16, 16, 18, 18, 18, 18, 3, 5, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 2, 5, 6, 7, 8, 9, 10, 11, 12, 45, 14, 47, 48, 49, 50, 51, 52, 46, 15, 13] set([0, 1, 3, 4, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71]) total number of confs: 86 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486655 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001154486655 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486655/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486655/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486655 Building ZINC001154486655 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486655' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486655 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001154486655 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486655/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486655 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 814) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/814: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCC[C@H]1[C@H](CNC(=O)OC(C)(C)C)Cc1ccccc1) `ZINC001154486655.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001154486655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486655/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 75 natoms 74 natoms 73 natoms 72 names: ZINC001154486655 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCC[C@H]1[C@H](CNC(=O)OC(C)(C)C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', '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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 9, 15, 15, 17, 17, 17, 17, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [16, 2, 5, 6, 7, 8, 9, 10, 11, 12, 45, 14, 47, 48, 49, 50, 51, 52, 46, 15, 13] set([0, 1, 3, 4, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71]) total number of confs: 74 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486655 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486655/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486655 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 815) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/815: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCC[C@H]1[C@H](CNC(=O)OC(C)(C)C)Cc1ccccc1) `ZINC001154486655.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001154486655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486655/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 75 natoms 74 natoms 73 natoms 72 names: ZINC001154486655 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCC[C@H]1[C@H](CNC(=O)OC(C)(C)C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', '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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 10, 16, 16, 18, 18, 18, 18, 3, 5, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 2, 5, 6, 7, 8, 9, 10, 11, 12, 45, 14, 47, 48, 49, 50, 51, 52, 46, 15, 13] set([0, 1, 3, 4, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71]) total number of confs: 86 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486655 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001154486655 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486655/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486655/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154486655 Building ZINC001154523646 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154523646' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154523646 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001154523646 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154523646/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154523646 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 816) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/816 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/816' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC(CCCCCNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC001154523646.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001154523646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154523646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001154523646 none CC(C)(C)OC(=O)N1CCC(CCCCCNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 41, 50, 41, 41, 41, 22, 16, 18, 16, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 41, 41, 41, 41, 18, 18, 18, 18, 18, 18, 18, 18, 9, 9, 2, 2, 2, 41, 41, 41, 41] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154523646 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154523646/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154523646 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 817) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/817 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/817' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC(CCCCCNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC001154523646.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001154523646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154523646/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001154523646 none CC(C)(C)OC(=O)N1CCC(CCCCCNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 50, 40, 40, 40, 22, 16, 18, 16, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 40, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 40, 40, 40, 40, 40, 18, 18, 18, 18, 18, 18, 18, 18, 9, 9, 2, 2, 2, 40, 40, 40, 40] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154523646 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001154523646 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154523646/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154523646/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154523646 Building ZINC001154523646 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154523646' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154523646 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001154523646 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154523646/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154523646 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 816) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/816: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC(CCCCCNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC001154523646.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001154523646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154523646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001154523646 none CC(C)(C)OC(=O)N1CCC(CCCCCNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 41, 50, 41, 41, 41, 22, 16, 18, 16, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 41, 41, 41, 41, 18, 18, 18, 18, 18, 18, 18, 18, 9, 9, 2, 2, 2, 41, 41, 41, 41] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154523646 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154523646/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154523646 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 817) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/817: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC(CCCCCNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC001154523646.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001154523646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154523646/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001154523646 none CC(C)(C)OC(=O)N1CCC(CCCCCNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 50, 40, 40, 40, 22, 16, 18, 16, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 40, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 40, 40, 40, 40, 40, 18, 18, 18, 18, 18, 18, 18, 18, 9, 9, 2, 2, 2, 40, 40, 40, 40] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154523646 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001154523646 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154523646/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154523646/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154523646 Building ZINC001154753920 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154753920' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154753920 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001154753920 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154753920/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154753920 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 818) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/818 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/818' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(CN2CCCC2)c(C(F)(F)F)c1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001154753920.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001154753920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154753920/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001154753920 none O=C(Nc1ccc(CN2CCCC2)c(C(F)(F)F)c1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 10, 5, 5, 5, 5, 1, 5, 15, 15, 15, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 10, 10, 10, 25, 29, 29, 29, 29, 10, 10, 10, 10, 10, 10, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 10, 10, 25, 25, 29, 29, 29, 29, 29, 29, 29, 29, 10, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154753920 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154753920/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154753920 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 819) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/819 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/819' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(CN2CCCC2)c(C(F)(F)F)c1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001154753920.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001154753920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154753920/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001154753920 none O=C(Nc1ccc(CN2CCCC2)c(C(F)(F)F)c1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 10, 5, 5, 5, 5, 1, 5, 15, 15, 15, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 10, 4, 10, 24, 30, 30, 30, 30, 10, 10, 10, 10, 10, 10, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 10, 10, 24, 24, 30, 30, 30, 30, 30, 30, 30, 30, 10, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154753920 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001154753920 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154753920/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154753920/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154753920 Building ZINC001154753920 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154753920' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154753920 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001154753920 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154753920/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154753920 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 818) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/818: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(CN2CCCC2)c(C(F)(F)F)c1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001154753920.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001154753920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154753920/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001154753920 none O=C(Nc1ccc(CN2CCCC2)c(C(F)(F)F)c1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 10, 5, 5, 5, 5, 1, 5, 15, 15, 15, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 10, 10, 10, 25, 29, 29, 29, 29, 10, 10, 10, 10, 10, 10, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 10, 10, 25, 25, 29, 29, 29, 29, 29, 29, 29, 29, 10, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154753920 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154753920/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154753920 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 819) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/819: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(CN2CCCC2)c(C(F)(F)F)c1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001154753920.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001154753920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154753920/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001154753920 none O=C(Nc1ccc(CN2CCCC2)c(C(F)(F)F)c1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 10, 5, 5, 5, 5, 1, 5, 15, 15, 15, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 10, 4, 10, 24, 30, 30, 30, 30, 10, 10, 10, 10, 10, 10, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 10, 10, 24, 24, 30, 30, 30, 30, 30, 30, 30, 30, 10, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154753920 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001154753920 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154753920/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154753920/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001154753920 Building ZINC001155006931 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155006931' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155006931 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001155006931 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155006931/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155006931 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 820) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/820 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/820' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1c[nH]c2ccc(Br)cc12)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001155006931.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001155006931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155006931/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001155006931 none O=C(Nc1c[nH]c2ccc(Br)cc12)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 12, 12, 12, 12, 12, 6, 26, 26, 26, 26, 12, 12] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155006931 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155006931/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155006931 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 821) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/821 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/821' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1c[nH]c2ccc(Br)cc12)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001155006931.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001155006931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155006931/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001155006931 none O=C(Nc1c[nH]c2ccc(Br)cc12)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 11, 11, 11, 11, 11, 6, 25, 25, 25, 25, 11, 11] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155006931 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001155006931 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155006931/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155006931/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155006931 Building ZINC001155006931 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155006931' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155006931 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001155006931 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155006931/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155006931 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 820) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/820: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1c[nH]c2ccc(Br)cc12)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001155006931.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001155006931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155006931/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001155006931 none O=C(Nc1c[nH]c2ccc(Br)cc12)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 12, 12, 12, 12, 12, 6, 26, 26, 26, 26, 12, 12] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155006931 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155006931/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155006931 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 821) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/821: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1c[nH]c2ccc(Br)cc12)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001155006931.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001155006931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155006931/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001155006931 none O=C(Nc1c[nH]c2ccc(Br)cc12)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 11, 11, 11, 11, 11, 6, 25, 25, 25, 25, 11, 11] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155006931 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001155006931 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155006931/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155006931/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155006931 Building ZINC001155026657 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155026657' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155026657 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001155026657 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155026657/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155026657 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 822) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/822 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/822' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)Nc1sc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)nc1c1ccccc1) `ZINC001155026657.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001155026657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155026657/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001155026657 none CC(=O)Nc1sc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)nc1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'C.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'] dock atom type numbers: [5, 1, 11, 8, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens 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, 12, 12, 12, 6, 6, 1, 6, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 12, 12, 12, 25, 25, 20, 25, 25, 21, 21, 21, 21, 6, 6, 1, 6, 25, 25, 20, 25, 25] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155026657 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155026657/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155026657 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 823) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/823 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/823' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)Nc1sc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)nc1c1ccccc1) `ZINC001155026657.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001155026657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155026657/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001155026657 none CC(=O)Nc1sc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)nc1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'C.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'] dock atom type numbers: [5, 1, 11, 8, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens 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, 12, 12, 12, 6, 6, 1, 6, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 12, 12, 12, 25, 25, 20, 25, 25, 21, 21, 21, 21, 6, 6, 1, 6, 25, 25, 20, 25, 25] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155026657 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001155026657 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155026657/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155026657/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155026657 Building ZINC001155026657 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155026657' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155026657 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001155026657 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155026657/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155026657 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 822) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/822: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)Nc1sc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)nc1c1ccccc1) `ZINC001155026657.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001155026657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155026657/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001155026657 none CC(=O)Nc1sc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)nc1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'C.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'] dock atom type numbers: [5, 1, 11, 8, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens 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, 12, 12, 12, 6, 6, 1, 6, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 12, 12, 12, 25, 25, 20, 25, 25, 21, 21, 21, 21, 6, 6, 1, 6, 25, 25, 20, 25, 25] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155026657 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155026657/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155026657 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 823) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/823: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)Nc1sc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)nc1c1ccccc1) `ZINC001155026657.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001155026657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155026657/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001155026657 none CC(=O)Nc1sc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)nc1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'C.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'] dock atom type numbers: [5, 1, 11, 8, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens 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, 12, 12, 12, 6, 6, 1, 6, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 12, 12, 12, 25, 25, 20, 25, 25, 21, 21, 21, 21, 6, 6, 1, 6, 25, 25, 20, 25, 25] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155026657 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001155026657 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155026657/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155026657/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155026657 Building ZINC001155287829 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155287829' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155287829 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001155287829 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155287829/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155287829 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 824) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/824 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/824' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N(CCNC(=O)OC(C)(C)C)Cc1cccc(Cl)c1) `ZINC001155287829.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001155287829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155287829/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001155287829 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N(CCNC(=O)OC(C)(C)C)Cc1cccc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 16, 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, 9, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 6, 17, 24, 24, 31, 31, 31, 31, 2, 2, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 17, 31, 31, 31, 31, 31, 31, 31, 31, 31, 2, 2, 6, 6, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 32, 33, 6, 7, 8, 9, 10, 36, 12, 34, 11, 35, 4, 5, 31] set([13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 106 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155287829 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155287829/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155287829 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 825) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/825 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/825' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N(CCNC(=O)OC(C)(C)C)Cc1cccc(Cl)c1) `ZINC001155287829.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001155287829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155287829/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001155287829 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N(CCNC(=O)OC(C)(C)C)Cc1cccc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 16, 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, 9, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 6, 16, 22, 22, 32, 32, 32, 32, 2, 2, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 16, 32, 32, 32, 32, 32, 32, 32, 32, 32, 2, 2, 6, 6, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 32, 33, 6, 7, 8, 9, 10, 36, 12, 34, 11, 35, 4, 5, 31] set([13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 104 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155287829 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001155287829 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155287829/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155287829/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155287829 Building ZINC001155287829 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155287829' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155287829 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001155287829 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155287829/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155287829 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 824) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/824: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N(CCNC(=O)OC(C)(C)C)Cc1cccc(Cl)c1) `ZINC001155287829.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001155287829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155287829/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001155287829 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N(CCNC(=O)OC(C)(C)C)Cc1cccc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 16, 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, 9, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 6, 17, 24, 24, 31, 31, 31, 31, 2, 2, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 17, 31, 31, 31, 31, 31, 31, 31, 31, 31, 2, 2, 6, 6, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 32, 33, 6, 7, 8, 9, 10, 36, 12, 34, 11, 35, 4, 5, 31] set([13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 106 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155287829 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155287829/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155287829 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 825) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/825: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N(CCNC(=O)OC(C)(C)C)Cc1cccc(Cl)c1) `ZINC001155287829.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001155287829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155287829/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001155287829 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N(CCNC(=O)OC(C)(C)C)Cc1cccc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 16, 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, 9, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 6, 16, 22, 22, 32, 32, 32, 32, 2, 2, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 16, 32, 32, 32, 32, 32, 32, 32, 32, 32, 2, 2, 6, 6, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 32, 33, 6, 7, 8, 9, 10, 36, 12, 34, 11, 35, 4, 5, 31] set([13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 104 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155287829 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001155287829 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155287829/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155287829/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155287829 Building ZINC001155351215 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155351215' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155351215 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001155351215 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155351215/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155351215 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 826) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/826 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/826' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)CC[C@H]1Cc2ccccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1) `ZINC001155351215.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001155351215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155351215/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001155351215 none CC(C)(C)OC(=O)CC[C@H]1Cc2ccccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 36, 9, 36, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 3, 1, 1, 1, 2, 2, 2, 2, 2, 3, 39, 39, 39, 39, 39, 39, 39, 39, 39, 9, 9, 6, 6, 3, 3, 3, 3, 3, 3, 2, 2, 3, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 116 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155351215 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155351215/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155351215 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 827) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/827 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/827' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)CC[C@H]1Cc2ccccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1) `ZINC001155351215.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001155351215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155351215/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001155351215 none CC(C)(C)OC(=O)CC[C@H]1Cc2ccccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 31, 8, 31, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 35, 35, 35, 35, 35, 35, 35, 35, 35, 8, 8, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155351215 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001155351215 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155351215/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155351215/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155351215 Building ZINC001155351215 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155351215' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155351215 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001155351215 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155351215/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155351215 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 826) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/826: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)CC[C@H]1Cc2ccccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1) `ZINC001155351215.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001155351215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155351215/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001155351215 none CC(C)(C)OC(=O)CC[C@H]1Cc2ccccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 36, 9, 36, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 3, 1, 1, 1, 2, 2, 2, 2, 2, 3, 39, 39, 39, 39, 39, 39, 39, 39, 39, 9, 9, 6, 6, 3, 3, 3, 3, 3, 3, 2, 2, 3, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 116 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155351215 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155351215/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155351215 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 827) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/827: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)CC[C@H]1Cc2ccccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1) `ZINC001155351215.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001155351215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155351215/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001155351215 none CC(C)(C)OC(=O)CC[C@H]1Cc2ccccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 31, 8, 31, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 35, 35, 35, 35, 35, 35, 35, 35, 35, 8, 8, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155351215 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001155351215 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155351215/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155351215/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155351215 Building ZINC001155351216 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155351216' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155351216 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001155351216 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155351216/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155351216 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 828) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/828 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/828' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)CC[C@@H]1Cc2ccccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1) `ZINC001155351216.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001155351216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155351216/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001155351216 none CC(C)(C)OC(=O)CC[C@@H]1Cc2ccccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 32, 8, 32, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 34, 34, 34, 34, 34, 34, 34, 34, 34, 8, 8, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155351216 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155351216/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155351216 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 829) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/829 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/829' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)CC[C@@H]1Cc2ccccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1) `ZINC001155351216.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001155351216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155351216/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001155351216 none CC(C)(C)OC(=O)CC[C@@H]1Cc2ccccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 35, 9, 35, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 1, 1, 1, 2, 2, 2, 2, 2, 3, 38, 38, 38, 38, 38, 38, 38, 38, 38, 9, 9, 7, 7, 3, 3, 3, 3, 3, 3, 2, 2, 3, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 116 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155351216 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001155351216 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155351216/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155351216/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155351216 Building ZINC001155351216 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155351216' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155351216 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001155351216 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155351216/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155351216 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 828) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/828: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)CC[C@@H]1Cc2ccccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1) `ZINC001155351216.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001155351216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155351216/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001155351216 none CC(C)(C)OC(=O)CC[C@@H]1Cc2ccccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 32, 8, 32, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 34, 34, 34, 34, 34, 34, 34, 34, 34, 8, 8, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155351216 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155351216/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155351216 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 829) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/829: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)CC[C@@H]1Cc2ccccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1) `ZINC001155351216.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001155351216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155351216/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001155351216 none CC(C)(C)OC(=O)CC[C@@H]1Cc2ccccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 35, 9, 35, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 1, 1, 1, 2, 2, 2, 2, 2, 3, 38, 38, 38, 38, 38, 38, 38, 38, 38, 9, 9, 7, 7, 3, 3, 3, 3, 3, 3, 2, 2, 3, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 116 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155351216 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001155351216 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155351216/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155351216/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155351216 Building ZINC001155367230 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001155367230 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 830) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/830 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/830' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCOc1ccccc1)Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1) `ZINC001155367230.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001155367230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001155367230 none CN(CCOc1ccccc1)Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 27, 27, 27, 27, 27, 27, 4, 1, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 10, 10, 10, 14, 14, 14, 14, 27, 27, 27, 27, 27, 8, 8, 4, 4, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4] 50 rigid atoms, others: [48, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 831) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/831 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/831' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCOc1ccccc1)Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1) `ZINC001155367230.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001155367230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001155367230 none CN(CCOc1ccccc1)Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 27, 27, 27, 27, 27, 27, 4, 1, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 10, 10, 10, 14, 14, 14, 14, 27, 27, 27, 27, 27, 8, 8, 4, 4, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4] 50 rigid atoms, others: [48, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 832) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/832 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/832' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCOc1ccccc1)Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1) `ZINC001155367230.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001155367230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001155367230 none CN(CCOc1ccccc1)Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 13, 13, 26, 26, 26, 26, 26, 26, 1, 1, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 9, 9, 9, 13, 13, 13, 13, 26, 26, 26, 26, 26, 8, 8, 4, 4, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4] 50 rigid atoms, others: [48, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 833) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/833 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/833' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCOc1ccccc1)Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1) `ZINC001155367230.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001155367230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001155367230 none CN(CCOc1ccccc1)Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 13, 13, 26, 26, 26, 26, 26, 26, 1, 1, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 9, 9, 9, 13, 13, 13, 13, 26, 26, 26, 26, 26, 8, 8, 4, 4, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4] 50 rigid atoms, others: [48, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001155367230 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230 Building ZINC001155367230 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001155367230 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 830) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/830: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCOc1ccccc1)Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1) `ZINC001155367230.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001155367230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001155367230 none CN(CCOc1ccccc1)Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 27, 27, 27, 27, 27, 27, 4, 1, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 10, 10, 10, 14, 14, 14, 14, 27, 27, 27, 27, 27, 8, 8, 4, 4, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4] 50 rigid atoms, others: [48, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 831) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/831: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCOc1ccccc1)Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1) `ZINC001155367230.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001155367230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001155367230 none CN(CCOc1ccccc1)Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 27, 27, 27, 27, 27, 27, 4, 1, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 10, 10, 10, 14, 14, 14, 14, 27, 27, 27, 27, 27, 8, 8, 4, 4, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4] 50 rigid atoms, others: [48, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 832) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/832: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCOc1ccccc1)Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1) `ZINC001155367230.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001155367230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001155367230 none CN(CCOc1ccccc1)Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 13, 13, 26, 26, 26, 26, 26, 26, 1, 1, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 9, 9, 9, 13, 13, 13, 13, 26, 26, 26, 26, 26, 8, 8, 4, 4, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4] 50 rigid atoms, others: [48, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 833) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/833: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCOc1ccccc1)Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1) `ZINC001155367230.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001155367230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001155367230 none CN(CCOc1ccccc1)Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 13, 13, 26, 26, 26, 26, 26, 26, 1, 1, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 9, 9, 9, 13, 13, 13, 13, 26, 26, 26, 26, 26, 8, 8, 4, 4, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4] 50 rigid atoms, others: [48, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001155367230 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230 Building ZINC001155367230 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001155367230 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 830) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/830: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCOc1ccccc1)Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1) `ZINC001155367230.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001155367230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001155367230 none CN(CCOc1ccccc1)Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 27, 27, 27, 27, 27, 27, 4, 1, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 10, 10, 10, 14, 14, 14, 14, 27, 27, 27, 27, 27, 8, 8, 4, 4, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4] 50 rigid atoms, others: [48, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 831) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/831: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCOc1ccccc1)Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1) `ZINC001155367230.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001155367230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001155367230 none CN(CCOc1ccccc1)Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 27, 27, 27, 27, 27, 27, 4, 1, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 10, 10, 10, 14, 14, 14, 14, 27, 27, 27, 27, 27, 8, 8, 4, 4, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4] 50 rigid atoms, others: [48, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 832) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/832: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCOc1ccccc1)Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1) `ZINC001155367230.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001155367230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001155367230 none CN(CCOc1ccccc1)Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 13, 13, 26, 26, 26, 26, 26, 26, 1, 1, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 9, 9, 9, 13, 13, 13, 13, 26, 26, 26, 26, 26, 8, 8, 4, 4, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4] 50 rigid atoms, others: [48, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 833) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/833: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCOc1ccccc1)Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1) `ZINC001155367230.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001155367230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001155367230 none CN(CCOc1ccccc1)Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 13, 13, 26, 26, 26, 26, 26, 26, 1, 1, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 9, 9, 9, 13, 13, 13, 13, 26, 26, 26, 26, 26, 8, 8, 4, 4, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4] 50 rigid atoms, others: [48, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001155367230 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230 Building ZINC001155367230 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001155367230 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 830) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/830: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCOc1ccccc1)Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1) `ZINC001155367230.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001155367230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001155367230 none CN(CCOc1ccccc1)Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 27, 27, 27, 27, 27, 27, 4, 1, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 10, 10, 10, 14, 14, 14, 14, 27, 27, 27, 27, 27, 8, 8, 4, 4, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4] 50 rigid atoms, others: [48, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 831) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/831: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCOc1ccccc1)Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1) `ZINC001155367230.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001155367230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001155367230 none CN(CCOc1ccccc1)Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 27, 27, 27, 27, 27, 27, 4, 1, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 10, 10, 10, 14, 14, 14, 14, 27, 27, 27, 27, 27, 8, 8, 4, 4, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4] 50 rigid atoms, others: [48, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 832) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/832: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCOc1ccccc1)Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1) `ZINC001155367230.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001155367230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001155367230 none CN(CCOc1ccccc1)Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 13, 13, 26, 26, 26, 26, 26, 26, 1, 1, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 9, 9, 9, 13, 13, 13, 13, 26, 26, 26, 26, 26, 8, 8, 4, 4, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4] 50 rigid atoms, others: [48, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 833) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/833: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCOc1ccccc1)Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1) `ZINC001155367230.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001155367230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001155367230 none CN(CCOc1ccccc1)Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 13, 13, 26, 26, 26, 26, 26, 26, 1, 1, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 9, 9, 9, 13, 13, 13, 13, 26, 26, 26, 26, 26, 8, 8, 4, 4, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4] 50 rigid atoms, others: [48, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001155367230 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155367230 Building ZINC001155863450 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155863450' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155863450 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001155863450 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155863450/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155863450 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 834) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/834 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/834' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](c2cccc(C(F)(F)F)c2)C1) `ZINC001155863450.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001155863450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155863450/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001155863450 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](c2cccc(C(F)(F)F)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 50, 50, 25, 50, 50, 50, 50, 50, 50, 9, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 9, 9, 50, 50, 31, 50, 9, 9] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155863450 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155863450/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155863450 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 835) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/835 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/835' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](c2cccc(C(F)(F)F)c2)C1) `ZINC001155863450.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001155863450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155863450/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001155863450 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](c2cccc(C(F)(F)F)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 50, 50, 8, 50, 50, 50, 50, 50, 50, 8, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 8, 8, 50, 50, 8, 50, 8, 8] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155863450 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001155863450 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155863450/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155863450/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155863450 Building ZINC001155863450 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155863450' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155863450 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001155863450 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155863450/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155863450 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 834) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/834: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](c2cccc(C(F)(F)F)c2)C1) `ZINC001155863450.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001155863450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155863450/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001155863450 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](c2cccc(C(F)(F)F)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 50, 50, 25, 50, 50, 50, 50, 50, 50, 9, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 9, 9, 50, 50, 31, 50, 9, 9] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155863450 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155863450/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155863450 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 835) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/835: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](c2cccc(C(F)(F)F)c2)C1) `ZINC001155863450.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001155863450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155863450/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001155863450 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](c2cccc(C(F)(F)F)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 50, 50, 8, 50, 50, 50, 50, 50, 50, 8, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 8, 8, 50, 50, 8, 50, 8, 8] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155863450 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001155863450 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155863450/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155863450/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001155863450 Building ZINC001156015803 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156015803' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156015803 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001156015803 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156015803/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156015803 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 836) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/836 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/836' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1C[C@H](c2ccc(C(F)(F)F)cc2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001156015803.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001156015803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156015803/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001156015803 none O=C(N[C@H]1C[C@H](c2ccc(C(F)(F)F)cc2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 16, 17, 17, 17, 17, 38, 38, 17, 17, 38, 38, 38, 38, 38, 17, 1, 1, 1, 8, 8, 8, 8, 8, 4, 17, 17, 38, 38, 38, 38, 17, 17, 8, 8] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156015803 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156015803/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156015803 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 837) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/837 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/837' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1C[C@H](c2ccc(C(F)(F)F)cc2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001156015803.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001156015803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156015803/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001156015803 none O=C(N[C@H]1C[C@H](c2ccc(C(F)(F)F)cc2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 5, 15, 16, 16, 16, 16, 38, 38, 16, 16, 38, 38, 38, 38, 38, 16, 1, 1, 1, 8, 8, 8, 8, 8, 4, 16, 16, 38, 38, 38, 38, 16, 16, 8, 8] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156015803 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001156015803 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156015803/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156015803/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156015803 Building ZINC001156015803 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156015803' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156015803 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001156015803 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156015803/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156015803 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 836) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/836: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1C[C@H](c2ccc(C(F)(F)F)cc2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001156015803.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001156015803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156015803/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001156015803 none O=C(N[C@H]1C[C@H](c2ccc(C(F)(F)F)cc2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 16, 17, 17, 17, 17, 38, 38, 17, 17, 38, 38, 38, 38, 38, 17, 1, 1, 1, 8, 8, 8, 8, 8, 4, 17, 17, 38, 38, 38, 38, 17, 17, 8, 8] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156015803 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156015803/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156015803 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 837) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/837: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1C[C@H](c2ccc(C(F)(F)F)cc2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001156015803.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001156015803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156015803/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001156015803 none O=C(N[C@H]1C[C@H](c2ccc(C(F)(F)F)cc2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 5, 15, 16, 16, 16, 16, 38, 38, 16, 16, 38, 38, 38, 38, 38, 16, 1, 1, 1, 8, 8, 8, 8, 8, 4, 16, 16, 38, 38, 38, 38, 16, 16, 8, 8] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156015803 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001156015803 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156015803/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156015803/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156015803 Building ZINC001156065637 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156065637' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156065637 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001156065637 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156065637/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156065637 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 838) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/838 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/838' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)sc1Cc1ccc(F)cc1F) `ZINC001156065637.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001156065637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156065637/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001156065637 none Cc1nc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)sc1Cc1ccc(F)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 14, 1, 5, 1, 1, 1, 1, 15, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 20, 27, 27, 27, 27, 27, 27, 27, 6, 6, 6, 3, 4, 4, 4, 4, 20, 20, 27, 27, 27] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156065637 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156065637/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156065637 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 839) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/839 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/839' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)sc1Cc1ccc(F)cc1F) `ZINC001156065637.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001156065637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156065637/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001156065637 none Cc1nc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)sc1Cc1ccc(F)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 14, 1, 5, 1, 1, 1, 1, 15, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 20, 27, 27, 27, 27, 27, 27, 27, 6, 6, 6, 3, 4, 4, 4, 4, 20, 20, 27, 27, 27] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156065637 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001156065637 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156065637/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156065637/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156065637 Building ZINC001156065637 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156065637' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156065637 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001156065637 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156065637/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156065637 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 838) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/838: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)sc1Cc1ccc(F)cc1F) `ZINC001156065637.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001156065637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156065637/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001156065637 none Cc1nc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)sc1Cc1ccc(F)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 14, 1, 5, 1, 1, 1, 1, 15, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 20, 27, 27, 27, 27, 27, 27, 27, 6, 6, 6, 3, 4, 4, 4, 4, 20, 20, 27, 27, 27] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156065637 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156065637/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156065637 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 839) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/839: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)sc1Cc1ccc(F)cc1F) `ZINC001156065637.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001156065637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156065637/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001156065637 none Cc1nc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)sc1Cc1ccc(F)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 14, 1, 5, 1, 1, 1, 1, 15, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 20, 27, 27, 27, 27, 27, 27, 27, 6, 6, 6, 3, 4, 4, 4, 4, 20, 20, 27, 27, 27] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156065637 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001156065637 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156065637/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156065637/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156065637 Building ZINC001156313650 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156313650' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156313650 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001156313650 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156313650/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156313650 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 840) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/840 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/840' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H]1c1cncc(Br)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001156313650.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001156313650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156313650/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001156313650 none O=C(N1CCC[C@H]1c1cncc(Br)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 1, 8, 1, 1, 17, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 9, 17, 17, 17, 17, 17, 17, 49, 49, 49, 49, 49, 49, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 17, 17, 17, 17, 17, 17, 49, 49, 49, 3, 1, 3] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156313650 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156313650/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156313650 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 841) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/841 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/841' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H]1c1cncc(Br)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001156313650.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001156313650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156313650/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001156313650 none O=C(N1CCC[C@H]1c1cncc(Br)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 1, 8, 1, 1, 17, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 14, 14, 14, 14, 14, 14, 45, 45, 45, 45, 45, 45, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 14, 14, 14, 14, 14, 14, 45, 45, 45, 3, 1, 3] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 74 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156313650 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001156313650 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156313650/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156313650/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156313650 Building ZINC001156313650 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156313650' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156313650 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001156313650 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156313650/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156313650 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 840) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/840: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H]1c1cncc(Br)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001156313650.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001156313650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156313650/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001156313650 none O=C(N1CCC[C@H]1c1cncc(Br)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 1, 8, 1, 1, 17, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 9, 17, 17, 17, 17, 17, 17, 49, 49, 49, 49, 49, 49, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 17, 17, 17, 17, 17, 17, 49, 49, 49, 3, 1, 3] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156313650 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156313650/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156313650 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 841) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/841: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H]1c1cncc(Br)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001156313650.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001156313650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156313650/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001156313650 none O=C(N1CCC[C@H]1c1cncc(Br)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 1, 8, 1, 1, 17, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 14, 14, 14, 14, 14, 14, 45, 45, 45, 45, 45, 45, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 14, 14, 14, 14, 14, 14, 45, 45, 45, 3, 1, 3] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 74 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156313650 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001156313650 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156313650/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156313650/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156313650 Building ZINC001156313651 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156313651' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156313651 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001156313651 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156313651/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156313651 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 842) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/842 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/842' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H]1c1cncc(Br)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001156313651.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001156313651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156313651/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001156313651 none O=C(N1CCC[C@@H]1c1cncc(Br)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 1, 8, 1, 1, 17, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 13, 13, 13, 13, 13, 13, 45, 45, 45, 45, 45, 45, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 13, 13, 13, 13, 13, 13, 45, 45, 45, 3, 1, 3] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 75 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156313651 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156313651/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156313651 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 843) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/843 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/843' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H]1c1cncc(Br)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001156313651.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001156313651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156313651/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001156313651 none O=C(N1CCC[C@@H]1c1cncc(Br)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 1, 8, 1, 1, 17, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 9, 17, 17, 17, 17, 17, 17, 48, 48, 48, 48, 48, 48, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 17, 17, 17, 17, 17, 17, 48, 48, 48, 3, 1, 3] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 80 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156313651 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001156313651 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156313651/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156313651/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156313651 Building ZINC001156313651 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156313651' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156313651 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001156313651 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156313651/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156313651 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 842) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/842: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H]1c1cncc(Br)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001156313651.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001156313651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156313651/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001156313651 none O=C(N1CCC[C@@H]1c1cncc(Br)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 1, 8, 1, 1, 17, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 13, 13, 13, 13, 13, 13, 45, 45, 45, 45, 45, 45, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 13, 13, 13, 13, 13, 13, 45, 45, 45, 3, 1, 3] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 75 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156313651 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156313651/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156313651 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 843) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/843: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H]1c1cncc(Br)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001156313651.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001156313651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156313651/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001156313651 none O=C(N1CCC[C@@H]1c1cncc(Br)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 1, 8, 1, 1, 17, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 9, 17, 17, 17, 17, 17, 17, 48, 48, 48, 48, 48, 48, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 17, 17, 17, 17, 17, 17, 48, 48, 48, 3, 1, 3] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 80 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156313651 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001156313651 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156313651/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156313651/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156313651 Building ZINC001156906317 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001156906317 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 844) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/844 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/844' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001156906317.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001156906317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001156906317 none O=C(N[C@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 7, 24, 24, 24, 24, 24, 24, 33, 33, 30, 33, 33, 33, 33, 24, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 24, 24, 24, 24, 24, 24, 33, 33, 33, 24, 24, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 845) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/845 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/845' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001156906317.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001156906317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001156906317 none O=C(N[C@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 18, 18, 18, 18, 18, 18, 28, 28, 28, 28, 28, 28, 28, 18, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 18, 18, 18, 18, 18, 18, 28, 28, 28, 18, 18, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 846) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/846 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/846' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001156906317.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001156906317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001156906317 none O=C(N[C@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 7, 24, 24, 24, 24, 24, 24, 33, 33, 30, 33, 33, 33, 33, 24, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 24, 24, 24, 24, 24, 24, 33, 33, 33, 24, 24, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 847) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/847 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/847' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001156906317.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001156906317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001156906317 none O=C(N[C@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 18, 18, 18, 18, 18, 18, 28, 28, 28, 28, 28, 28, 28, 18, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 18, 18, 18, 18, 18, 18, 28, 28, 28, 18, 18, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001156906317 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317 Building ZINC001156906317 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001156906317 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 844) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/844: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001156906317.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001156906317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001156906317 none O=C(N[C@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 7, 24, 24, 24, 24, 24, 24, 33, 33, 30, 33, 33, 33, 33, 24, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 24, 24, 24, 24, 24, 24, 33, 33, 33, 24, 24, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 845) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/845: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001156906317.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001156906317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001156906317 none O=C(N[C@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 18, 18, 18, 18, 18, 18, 28, 28, 28, 28, 28, 28, 28, 18, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 18, 18, 18, 18, 18, 18, 28, 28, 28, 18, 18, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 846) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/846: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001156906317.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001156906317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001156906317 none O=C(N[C@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 7, 24, 24, 24, 24, 24, 24, 33, 33, 30, 33, 33, 33, 33, 24, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 24, 24, 24, 24, 24, 24, 33, 33, 33, 24, 24, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 847) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/847: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001156906317.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001156906317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001156906317 none O=C(N[C@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 18, 18, 18, 18, 18, 18, 28, 28, 28, 28, 28, 28, 28, 18, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 18, 18, 18, 18, 18, 18, 28, 28, 28, 18, 18, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001156906317 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317 Building ZINC001156906317 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001156906317 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 844) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/844: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001156906317.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001156906317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001156906317 none O=C(N[C@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 7, 24, 24, 24, 24, 24, 24, 33, 33, 30, 33, 33, 33, 33, 24, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 24, 24, 24, 24, 24, 24, 33, 33, 33, 24, 24, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 845) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/845: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001156906317.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001156906317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001156906317 none O=C(N[C@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 18, 18, 18, 18, 18, 18, 28, 28, 28, 28, 28, 28, 28, 18, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 18, 18, 18, 18, 18, 18, 28, 28, 28, 18, 18, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 846) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/846: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001156906317.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001156906317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001156906317 none O=C(N[C@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 7, 24, 24, 24, 24, 24, 24, 33, 33, 30, 33, 33, 33, 33, 24, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 24, 24, 24, 24, 24, 24, 33, 33, 33, 24, 24, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 847) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/847: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001156906317.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001156906317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001156906317 none O=C(N[C@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 18, 18, 18, 18, 18, 18, 28, 28, 28, 28, 28, 28, 28, 18, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 18, 18, 18, 18, 18, 18, 28, 28, 28, 18, 18, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001156906317 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317 Building ZINC001156906317 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001156906317 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 844) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/844: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001156906317.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001156906317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001156906317 none O=C(N[C@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 7, 24, 24, 24, 24, 24, 24, 33, 33, 30, 33, 33, 33, 33, 24, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 24, 24, 24, 24, 24, 24, 33, 33, 33, 24, 24, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 845) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/845: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001156906317.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001156906317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001156906317 none O=C(N[C@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 18, 18, 18, 18, 18, 18, 28, 28, 28, 28, 28, 28, 28, 18, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 18, 18, 18, 18, 18, 18, 28, 28, 28, 18, 18, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 846) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/846: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001156906317.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001156906317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001156906317 none O=C(N[C@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 7, 24, 24, 24, 24, 24, 24, 33, 33, 30, 33, 33, 33, 33, 24, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 24, 24, 24, 24, 24, 24, 33, 33, 33, 24, 24, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 847) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/847: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001156906317.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001156906317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001156906317 none O=C(N[C@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 18, 18, 18, 18, 18, 18, 28, 28, 28, 28, 28, 28, 28, 18, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 18, 18, 18, 18, 18, 18, 28, 28, 28, 18, 18, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001156906317 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906317 Building ZINC001156906318 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001156906318 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 848) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/848 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/848' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001156906318.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001156906318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001156906318 none O=C(N[C@@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 9, 23, 23, 23, 23, 23, 23, 30, 30, 26, 26, 30, 30, 30, 23, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 23, 23, 23, 23, 23, 23, 30, 30, 30, 23, 23, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 849) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/849 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/849' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001156906318.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001156906318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001156906318 none O=C(N[C@@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 10, 25, 25, 25, 25, 25, 25, 33, 33, 30, 33, 33, 33, 33, 25, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 25, 25, 25, 25, 25, 25, 33, 33, 33, 25, 25, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 850) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/850 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/850' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001156906318.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001156906318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001156906318 none O=C(N[C@@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 9, 23, 23, 23, 23, 23, 23, 30, 30, 26, 26, 30, 30, 30, 23, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 23, 23, 23, 23, 23, 23, 30, 30, 30, 23, 23, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 851) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/851 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/851' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001156906318.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001156906318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001156906318 none O=C(N[C@@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 10, 25, 25, 25, 25, 25, 25, 33, 33, 30, 33, 33, 33, 33, 25, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 25, 25, 25, 25, 25, 25, 33, 33, 33, 25, 25, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001156906318 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318 Building ZINC001156906318 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001156906318 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 848) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/848: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001156906318.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001156906318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001156906318 none O=C(N[C@@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 9, 23, 23, 23, 23, 23, 23, 30, 30, 26, 26, 30, 30, 30, 23, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 23, 23, 23, 23, 23, 23, 30, 30, 30, 23, 23, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 849) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/849: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001156906318.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001156906318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001156906318 none O=C(N[C@@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 10, 25, 25, 25, 25, 25, 25, 33, 33, 30, 33, 33, 33, 33, 25, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 25, 25, 25, 25, 25, 25, 33, 33, 33, 25, 25, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 850) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/850: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001156906318.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001156906318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001156906318 none O=C(N[C@@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 9, 23, 23, 23, 23, 23, 23, 30, 30, 26, 26, 30, 30, 30, 23, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 23, 23, 23, 23, 23, 23, 30, 30, 30, 23, 23, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 851) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/851: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001156906318.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001156906318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001156906318 none O=C(N[C@@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 10, 25, 25, 25, 25, 25, 25, 33, 33, 30, 33, 33, 33, 33, 25, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 25, 25, 25, 25, 25, 25, 33, 33, 33, 25, 25, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001156906318 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318 Building ZINC001156906318 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001156906318 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 848) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/848: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001156906318.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001156906318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001156906318 none O=C(N[C@@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 9, 23, 23, 23, 23, 23, 23, 30, 30, 26, 26, 30, 30, 30, 23, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 23, 23, 23, 23, 23, 23, 30, 30, 30, 23, 23, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 849) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/849: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001156906318.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001156906318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001156906318 none O=C(N[C@@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 10, 25, 25, 25, 25, 25, 25, 33, 33, 30, 33, 33, 33, 33, 25, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 25, 25, 25, 25, 25, 25, 33, 33, 33, 25, 25, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 850) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/850: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001156906318.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001156906318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001156906318 none O=C(N[C@@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 9, 23, 23, 23, 23, 23, 23, 30, 30, 26, 26, 30, 30, 30, 23, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 23, 23, 23, 23, 23, 23, 30, 30, 30, 23, 23, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 851) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/851: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001156906318.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001156906318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001156906318 none O=C(N[C@@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 10, 25, 25, 25, 25, 25, 25, 33, 33, 30, 33, 33, 33, 33, 25, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 25, 25, 25, 25, 25, 25, 33, 33, 33, 25, 25, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001156906318 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318 Building ZINC001156906318 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001156906318 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 848) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/848: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001156906318.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001156906318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001156906318 none O=C(N[C@@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 9, 23, 23, 23, 23, 23, 23, 30, 30, 26, 26, 30, 30, 30, 23, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 23, 23, 23, 23, 23, 23, 30, 30, 30, 23, 23, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 849) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/849: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001156906318.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001156906318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001156906318 none O=C(N[C@@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 10, 25, 25, 25, 25, 25, 25, 33, 33, 30, 33, 33, 33, 33, 25, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 25, 25, 25, 25, 25, 25, 33, 33, 33, 25, 25, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 850) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/850: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001156906318.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001156906318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001156906318 none O=C(N[C@@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 9, 23, 23, 23, 23, 23, 23, 30, 30, 26, 26, 30, 30, 30, 23, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 23, 23, 23, 23, 23, 23, 30, 30, 30, 23, 23, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 851) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/851: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001156906318.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001156906318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001156906318 none O=C(N[C@@H]1CCCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 10, 25, 25, 25, 25, 25, 25, 33, 33, 30, 33, 33, 33, 33, 25, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 25, 25, 25, 25, 25, 25, 33, 33, 33, 25, 25, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001156906318 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001156906318 Building ZINC001157112680 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001157112680' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001157112680 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001157112680 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001157112680/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001157112680 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 852) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/852 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/852' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1Cl)c1cc(Cl)ccc1O) `ZINC001157112680.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001157112680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001157112680/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001157112680 none O=C(Nc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1Cl)c1cc(Cl)ccc1O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 16, 1, 1, 1, 16, 1, 1, 1, 12, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [22, 22, 10, 8, 10, 10, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 2, 3, 3, 10, 10, 10, 22, 50, 50, 50, 22, 50, 50, 50, 22, 10, 10, 2, 3, 3, 3, 3, 10, 50, 50, 50, 100] 100 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 336 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001157112680 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001157112680/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001157112680 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 853) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/853 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/853' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1Cl)c1cc(Cl)ccc1O) `ZINC001157112680.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001157112680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001157112680/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001157112680 none O=C(Nc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1Cl)c1cc(Cl)ccc1O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 16, 1, 1, 1, 16, 1, 1, 1, 12, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [27, 27, 13, 8, 13, 13, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 13, 13, 27, 50, 50, 50, 27, 50, 50, 50, 27, 13, 13, 2, 3, 3, 3, 3, 13, 50, 50, 50, 100] 100 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 333 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001157112680 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001157112680 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001157112680/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001157112680/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001157112680 Building ZINC001157112680 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001157112680' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001157112680 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001157112680 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001157112680/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001157112680 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 852) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/852: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1Cl)c1cc(Cl)ccc1O) `ZINC001157112680.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001157112680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001157112680/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001157112680 none O=C(Nc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1Cl)c1cc(Cl)ccc1O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 16, 1, 1, 1, 16, 1, 1, 1, 12, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [22, 22, 10, 8, 10, 10, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 2, 3, 3, 10, 10, 10, 22, 50, 50, 50, 22, 50, 50, 50, 22, 10, 10, 2, 3, 3, 3, 3, 10, 50, 50, 50, 100] 100 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 336 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001157112680 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001157112680/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001157112680 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 853) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/853: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1Cl)c1cc(Cl)ccc1O) `ZINC001157112680.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001157112680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001157112680/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001157112680 none O=C(Nc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1Cl)c1cc(Cl)ccc1O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 16, 1, 1, 1, 16, 1, 1, 1, 12, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [27, 27, 13, 8, 13, 13, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 13, 13, 27, 50, 50, 50, 27, 50, 50, 50, 27, 13, 13, 2, 3, 3, 3, 3, 13, 50, 50, 50, 100] 100 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 333 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001157112680 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001157112680 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001157112680/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001157112680/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001157112680 Building ZINC001159918385 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159918385' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159918385 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001159918385 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159918385/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159918385 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 854) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/854 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/854' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C[C@H](c2cccc(C(F)(F)F)c2)O1) `ZINC001159918385.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001159918385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159918385/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001159918385 none CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C[C@H](c2cccc(C(F)(F)F)c2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 6, 1, 7, 1, 1, 1, 3, 3, 3, 3, 3, 10, 10, 10, 10, 36, 36, 10, 36, 36, 36, 36, 36, 36, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 10, 10, 36, 36, 15, 36] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159918385 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159918385/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159918385 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 855) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/855 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/855' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C[C@H](c2cccc(C(F)(F)F)c2)O1) `ZINC001159918385.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001159918385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159918385/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001159918385 none CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C[C@H](c2cccc(C(F)(F)F)c2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 5, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 8, 8, 34, 34, 8, 34, 34, 34, 34, 34, 34, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 5, 8, 8, 34, 34, 8, 34] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159918385 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001159918385 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159918385/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159918385/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159918385 Building ZINC001159918385 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159918385' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159918385 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001159918385 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159918385/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159918385 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 854) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/854: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C[C@H](c2cccc(C(F)(F)F)c2)O1) `ZINC001159918385.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001159918385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159918385/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001159918385 none CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C[C@H](c2cccc(C(F)(F)F)c2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 6, 1, 7, 1, 1, 1, 3, 3, 3, 3, 3, 10, 10, 10, 10, 36, 36, 10, 36, 36, 36, 36, 36, 36, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 10, 10, 36, 36, 15, 36] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159918385 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159918385/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159918385 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 855) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/855: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C[C@H](c2cccc(C(F)(F)F)c2)O1) `ZINC001159918385.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001159918385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159918385/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001159918385 none CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C[C@H](c2cccc(C(F)(F)F)c2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 5, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 8, 8, 34, 34, 8, 34, 34, 34, 34, 34, 34, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 5, 8, 8, 34, 34, 8, 34] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159918385 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001159918385 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159918385/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159918385/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159918385 Building ZINC001159918386 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159918386' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159918386 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001159918386 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159918386/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159918386 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 856) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/856 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/856' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C[C@@H](c2cccc(C(F)(F)F)c2)O1) `ZINC001159918386.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001159918386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159918386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001159918386 none CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C[C@@H](c2cccc(C(F)(F)F)c2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 4, 2, 5, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 35, 35, 14, 35, 35, 35, 35, 35, 35, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 5, 7, 7, 35, 35, 21, 35] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159918386 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159918386/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159918386 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 857) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/857 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/857' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C[C@@H](c2cccc(C(F)(F)F)c2)O1) `ZINC001159918386.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001159918386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159918386/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001159918386 none CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C[C@@H](c2cccc(C(F)(F)F)c2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 5, 2, 6, 1, 1, 1, 3, 3, 3, 3, 3, 9, 9, 9, 9, 36, 36, 16, 36, 36, 36, 36, 36, 36, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 9, 9, 36, 36, 27, 36] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159918386 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001159918386 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159918386/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159918386/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159918386 Building ZINC001159918386 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159918386' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159918386 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001159918386 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159918386/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159918386 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 856) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/856: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C[C@@H](c2cccc(C(F)(F)F)c2)O1) `ZINC001159918386.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001159918386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159918386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001159918386 none CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C[C@@H](c2cccc(C(F)(F)F)c2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 4, 2, 5, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 35, 35, 14, 35, 35, 35, 35, 35, 35, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 5, 7, 7, 35, 35, 21, 35] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159918386 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159918386/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159918386 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 857) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/857: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C[C@@H](c2cccc(C(F)(F)F)c2)O1) `ZINC001159918386.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001159918386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159918386/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001159918386 none CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C[C@@H](c2cccc(C(F)(F)F)c2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 5, 2, 6, 1, 1, 1, 3, 3, 3, 3, 3, 9, 9, 9, 9, 36, 36, 16, 36, 36, 36, 36, 36, 36, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 9, 9, 36, 36, 27, 36] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159918386 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001159918386 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159918386/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159918386/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159918386 Building ZINC001159937283 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159937283' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159937283 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001159937283 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159937283/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159937283 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 858) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/858 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/858' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc([C@H](O)C2CCN(C(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cc1) `ZINC001159937283.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001159937283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159937283/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001159937283 none CCOc1ccc([C@H](O)C2CCN(C(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.ar', '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, 12, 1, 1, 1, 1, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 1, 1, 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, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [42, 42, 15, 15, 29, 29, 15, 6, 15, 15, 6, 6, 6, 2, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 6, 6, 29, 29, 42, 42, 42, 42, 42, 29, 29, 45, 6, 6, 6, 6, 6, 3, 1, 3, 6, 6, 6, 6, 29, 29] 150 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 208 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159937283 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159937283/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159937283 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 859) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/859 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/859' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc([C@H](O)C2CCN(C(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cc1) `ZINC001159937283.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001159937283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159937283/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001159937283 none CCOc1ccc([C@H](O)C2CCN(C(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.ar', '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, 12, 1, 1, 1, 1, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 1, 1, 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, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [44, 43, 21, 21, 34, 34, 21, 7, 21, 21, 7, 7, 7, 2, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 7, 7, 34, 34, 44, 44, 44, 44, 44, 34, 34, 63, 7, 7, 7, 7, 7, 3, 1, 3, 7, 7, 7, 7, 34, 34] 150 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 253 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159937283 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001159937283 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159937283/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159937283/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159937283 Building ZINC001159937283 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159937283' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159937283 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001159937283 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159937283/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159937283 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 858) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/858: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc([C@H](O)C2CCN(C(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cc1) `ZINC001159937283.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001159937283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159937283/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001159937283 none CCOc1ccc([C@H](O)C2CCN(C(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.ar', '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, 12, 1, 1, 1, 1, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 1, 1, 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, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [42, 42, 15, 15, 29, 29, 15, 6, 15, 15, 6, 6, 6, 2, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 6, 6, 29, 29, 42, 42, 42, 42, 42, 29, 29, 45, 6, 6, 6, 6, 6, 3, 1, 3, 6, 6, 6, 6, 29, 29] 150 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 208 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159937283 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159937283/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159937283 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 859) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/859: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc([C@H](O)C2CCN(C(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cc1) `ZINC001159937283.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001159937283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159937283/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001159937283 none CCOc1ccc([C@H](O)C2CCN(C(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.ar', '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, 12, 1, 1, 1, 1, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 1, 1, 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, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [44, 43, 21, 21, 34, 34, 21, 7, 21, 21, 7, 7, 7, 2, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 7, 7, 34, 34, 44, 44, 44, 44, 44, 34, 34, 63, 7, 7, 7, 7, 7, 3, 1, 3, 7, 7, 7, 7, 34, 34] 150 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 253 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159937283 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001159937283 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159937283/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159937283/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159937283 Building ZINC001159937284 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159937284' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159937284 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001159937284 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159937284/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159937284 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 860) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/860 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/860' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc([C@@H](O)C2CCN(C(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cc1) `ZINC001159937284.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001159937284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159937284/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001159937284 none CCOc1ccc([C@@H](O)C2CCN(C(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.ar', '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, 12, 1, 1, 1, 1, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 1, 1, 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, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [44, 43, 17, 17, 30, 30, 17, 6, 17, 17, 6, 6, 6, 2, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 6, 6, 30, 30, 44, 44, 44, 44, 44, 30, 30, 51, 6, 6, 6, 6, 6, 3, 1, 3, 6, 6, 6, 6, 30, 30] 150 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 222 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159937284 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159937284/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159937284 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 861) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/861 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/861' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc([C@@H](O)C2CCN(C(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cc1) `ZINC001159937284.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001159937284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159937284/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001159937284 none CCOc1ccc([C@@H](O)C2CCN(C(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.ar', '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, 12, 1, 1, 1, 1, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 1, 1, 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, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 32, 18, 32, 32, 18, 5, 18, 18, 5, 5, 5, 2, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 5, 5, 32, 32, 43, 43, 43, 43, 43, 32, 32, 54, 5, 5, 5, 5, 5, 3, 1, 3, 5, 5, 5, 5, 32, 32] 150 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 247 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159937284 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001159937284 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159937284/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159937284/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159937284 Building ZINC001159937284 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159937284' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159937284 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001159937284 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159937284/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159937284 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 860) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/860: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc([C@@H](O)C2CCN(C(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cc1) `ZINC001159937284.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001159937284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159937284/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001159937284 none CCOc1ccc([C@@H](O)C2CCN(C(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.ar', '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, 12, 1, 1, 1, 1, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 1, 1, 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, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [44, 43, 17, 17, 30, 30, 17, 6, 17, 17, 6, 6, 6, 2, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 6, 6, 30, 30, 44, 44, 44, 44, 44, 30, 30, 51, 6, 6, 6, 6, 6, 3, 1, 3, 6, 6, 6, 6, 30, 30] 150 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 222 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159937284 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159937284/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159937284 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 861) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/861: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc([C@@H](O)C2CCN(C(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cc1) `ZINC001159937284.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001159937284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159937284/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001159937284 none CCOc1ccc([C@@H](O)C2CCN(C(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.ar', '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, 12, 1, 1, 1, 1, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 1, 1, 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, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 32, 18, 32, 32, 18, 5, 18, 18, 5, 5, 5, 2, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 5, 5, 32, 32, 43, 43, 43, 43, 43, 32, 32, 54, 5, 5, 5, 5, 5, 3, 1, 3, 5, 5, 5, 5, 32, 32] 150 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 247 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159937284 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001159937284 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159937284/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159937284/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001159937284 Building ZINC001160449689 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160449689' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160449689 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001160449689 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160449689/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160449689 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 862) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/862 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/862' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(NS(=O)(=O)c2c(Cl)cccc2Cl)cc1)[C@]([O-])([SiH3])c1ccccc1) `ZINC001160449689.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001160449689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160449689/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001160449689 none O=C(Nc1ccc(NS(=O)(=O)c2c(Cl)cccc2Cl)cc1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 16, 1, 1, 1, 1, 16, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 5, 5, 2, 2, 20, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 5, 5, 1, 1, 1, 3, 3, 1, 3, 3, 2, 5, 5, 19, 50, 50, 50, 5, 5, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160449689 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160449689/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160449689 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 863) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/863 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/863' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(NS(=O)(=O)c2c(Cl)cccc2Cl)cc1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC001160449689.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001160449689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160449689/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001160449689 none O=C(Nc1ccc(NS(=O)(=O)c2c(Cl)cccc2Cl)cc1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 16, 1, 1, 1, 1, 16, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 6, 6, 2, 4, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 1, 1, 1, 3, 3, 1, 3, 3, 2, 6, 6, 21, 50, 50, 50, 6, 6, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160449689 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001160449689 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160449689/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160449689/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160449689 Building ZINC001160449689 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160449689' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160449689 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001160449689 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160449689/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160449689 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 862) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/862: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(NS(=O)(=O)c2c(Cl)cccc2Cl)cc1)[C@]([O-])([SiH3])c1ccccc1) `ZINC001160449689.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001160449689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160449689/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001160449689 none O=C(Nc1ccc(NS(=O)(=O)c2c(Cl)cccc2Cl)cc1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 16, 1, 1, 1, 1, 16, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 5, 5, 2, 2, 20, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 5, 5, 1, 1, 1, 3, 3, 1, 3, 3, 2, 5, 5, 19, 50, 50, 50, 5, 5, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160449689 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160449689/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160449689 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 863) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/863: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(NS(=O)(=O)c2c(Cl)cccc2Cl)cc1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC001160449689.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001160449689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160449689/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001160449689 none O=C(Nc1ccc(NS(=O)(=O)c2c(Cl)cccc2Cl)cc1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 16, 1, 1, 1, 1, 16, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 6, 6, 2, 4, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 1, 1, 1, 3, 3, 1, 3, 3, 2, 6, 6, 21, 50, 50, 50, 6, 6, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160449689 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001160449689 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160449689/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160449689/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160449689 Building ZINC001160980879 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160980879' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160980879 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001160980879 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160980879/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160980879 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 864) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/864 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/864' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](CC(C)C)C1) `ZINC001160980879.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001160980879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160980879/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001160980879 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](CC(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 20, 20, 3, 20, 20, 20, 20, 20, 20, 3, 3, 1, 1, 1, 2, 3, 4, 7, 7, 7, 7, 7, 7, 9, 9, 9, 7, 3, 3, 3, 20, 20, 3, 20, 3, 3, 3, 7, 7, 7, 7, 7, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 7] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 72 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160980879 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160980879/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160980879 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 865) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/865 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/865' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](CC(C)C)C1) `ZINC001160980879.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001160980879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160980879/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001160980879 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](CC(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 21, 21, 3, 21, 21, 21, 21, 21, 21, 3, 3, 1, 1, 1, 2, 4, 7, 9, 9, 9, 9, 9, 9, 12, 12, 12, 9, 3, 3, 3, 21, 21, 3, 21, 3, 3, 3, 9, 9, 9, 9, 9, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 9, 9] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 84 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160980879 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001160980879 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160980879/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160980879/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160980879 Building ZINC001160980879 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160980879' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160980879 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001160980879 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160980879/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160980879 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 864) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/864: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](CC(C)C)C1) `ZINC001160980879.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001160980879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160980879/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001160980879 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](CC(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 20, 20, 3, 20, 20, 20, 20, 20, 20, 3, 3, 1, 1, 1, 2, 3, 4, 7, 7, 7, 7, 7, 7, 9, 9, 9, 7, 3, 3, 3, 20, 20, 3, 20, 3, 3, 3, 7, 7, 7, 7, 7, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 7] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 72 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160980879 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160980879/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160980879 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 865) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/865: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](CC(C)C)C1) `ZINC001160980879.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001160980879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160980879/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001160980879 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](CC(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 21, 21, 3, 21, 21, 21, 21, 21, 21, 3, 3, 1, 1, 1, 2, 4, 7, 9, 9, 9, 9, 9, 9, 12, 12, 12, 9, 3, 3, 3, 21, 21, 3, 21, 3, 3, 3, 9, 9, 9, 9, 9, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 9, 9] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 84 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160980879 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001160980879 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160980879/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160980879/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160980879 Building ZINC001160980880 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160980880' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160980880 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001160980880 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160980880/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160980880 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 866) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/866 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/866' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](CC(C)C)C1) `ZINC001160980880.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001160980880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160980880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001160980880 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](CC(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 16, 16, 2, 16, 16, 16, 16, 16, 16, 2, 2, 1, 1, 1, 2, 4, 8, 8, 8, 8, 8, 8, 8, 12, 12, 12, 8, 2, 2, 2, 16, 16, 2, 16, 2, 2, 2, 8, 8, 8, 8, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 72 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160980880 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160980880/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160980880 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 867) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/867 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/867' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](CC(C)C)C1) `ZINC001160980880.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001160980880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160980880/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001160980880 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](CC(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 17, 17, 3, 17, 17, 17, 17, 17, 17, 3, 3, 1, 1, 1, 2, 3, 5, 8, 8, 8, 8, 8, 8, 13, 13, 13, 8, 3, 3, 3, 17, 17, 3, 17, 3, 3, 3, 8, 8, 8, 8, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 83 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160980880 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001160980880 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160980880/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160980880/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160980880 Building ZINC001160980880 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160980880' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160980880 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001160980880 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160980880/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160980880 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 866) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/866: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](CC(C)C)C1) `ZINC001160980880.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001160980880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160980880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001160980880 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](CC(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 16, 16, 2, 16, 16, 16, 16, 16, 16, 2, 2, 1, 1, 1, 2, 4, 8, 8, 8, 8, 8, 8, 8, 12, 12, 12, 8, 2, 2, 2, 16, 16, 2, 16, 2, 2, 2, 8, 8, 8, 8, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 72 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160980880 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160980880/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160980880 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 867) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/867: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](CC(C)C)C1) `ZINC001160980880.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001160980880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160980880/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001160980880 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](CC(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 17, 17, 3, 17, 17, 17, 17, 17, 17, 3, 3, 1, 1, 1, 2, 3, 5, 8, 8, 8, 8, 8, 8, 13, 13, 13, 8, 3, 3, 3, 17, 17, 3, 17, 3, 3, 3, 8, 8, 8, 8, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 83 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160980880 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001160980880 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160980880/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160980880/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001160980880 Building ZINC001161119089 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161119089' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161119089 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001161119089 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161119089/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161119089 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 868) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/868 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/868' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1O) `ZINC001161119089.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001161119089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161119089/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001161119089 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 25, 25, 4, 25, 25, 25, 25, 25, 25, 4, 4, 1, 1, 1, 1, 4, 4, 4, 8, 8, 7, 8, 8, 8, 8, 4, 4, 4, 25, 25, 4, 25, 4, 4, 4, 4, 8, 8, 8, 16] 100 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 96 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161119089 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161119089/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161119089 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 869) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/869 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/869' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1O) `ZINC001161119089.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001161119089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161119089/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001161119089 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 25, 25, 4, 25, 25, 25, 25, 25, 25, 4, 4, 1, 1, 1, 1, 4, 4, 4, 8, 8, 4, 8, 8, 8, 8, 4, 4, 4, 25, 25, 4, 25, 4, 4, 4, 4, 8, 8, 8, 16] 100 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 111 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161119089 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001161119089 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161119089/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161119089/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161119089 Building ZINC001161119089 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161119089' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161119089 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001161119089 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161119089/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161119089 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 868) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/868: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1O) `ZINC001161119089.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001161119089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161119089/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001161119089 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 25, 25, 4, 25, 25, 25, 25, 25, 25, 4, 4, 1, 1, 1, 1, 4, 4, 4, 8, 8, 7, 8, 8, 8, 8, 4, 4, 4, 25, 25, 4, 25, 4, 4, 4, 4, 8, 8, 8, 16] 100 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 96 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161119089 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161119089/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161119089 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 869) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/869: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1O) `ZINC001161119089.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001161119089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161119089/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001161119089 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 25, 25, 4, 25, 25, 25, 25, 25, 25, 4, 4, 1, 1, 1, 1, 4, 4, 4, 8, 8, 4, 8, 8, 8, 8, 4, 4, 4, 25, 25, 4, 25, 4, 4, 4, 4, 8, 8, 8, 16] 100 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 111 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161119089 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001161119089 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161119089/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161119089/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161119089 Building ZINC001161190874 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161190874' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161190874 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001161190874 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161190874/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161190874 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 870) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/870 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/870' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(C)(C(C)C)CC1) `ZINC001161190874.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001161190874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161190874/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001161190874 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(C)(C(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 18, 18, 2, 18, 18, 18, 18, 18, 18, 2, 2, 1, 1, 1, 2, 3, 3, 7, 7, 7, 7, 7, 8, 8, 7, 7, 2, 2, 2, 18, 18, 2, 18, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 8, 8, 8, 8, 8, 8, 8, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 60 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161190874 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161190874/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161190874 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 871) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/871 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/871' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(C)(C(C)C)CC1) `ZINC001161190874.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001161190874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161190874/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001161190874 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(C)(C(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 18, 18, 2, 18, 18, 18, 18, 18, 18, 2, 2, 1, 1, 1, 2, 4, 5, 8, 8, 8, 8, 8, 11, 11, 8, 8, 2, 2, 2, 18, 18, 2, 18, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 11, 11, 11, 11, 11, 11, 11, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 73 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161190874 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001161190874 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161190874/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161190874/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161190874 Building ZINC001161190874 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161190874' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161190874 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001161190874 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161190874/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161190874 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 870) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/870: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(C)(C(C)C)CC1) `ZINC001161190874.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001161190874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161190874/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001161190874 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(C)(C(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 18, 18, 2, 18, 18, 18, 18, 18, 18, 2, 2, 1, 1, 1, 2, 3, 3, 7, 7, 7, 7, 7, 8, 8, 7, 7, 2, 2, 2, 18, 18, 2, 18, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 8, 8, 8, 8, 8, 8, 8, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 60 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161190874 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161190874/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161190874 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 871) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/871: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(C)(C(C)C)CC1) `ZINC001161190874.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001161190874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161190874/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001161190874 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(C)(C(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 18, 18, 2, 18, 18, 18, 18, 18, 18, 2, 2, 1, 1, 1, 2, 4, 5, 8, 8, 8, 8, 8, 11, 11, 8, 8, 2, 2, 2, 18, 18, 2, 18, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 11, 11, 11, 11, 11, 11, 11, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 73 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161190874 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001161190874 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161190874/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161190874/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161190874 Building ZINC001161391385 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161391385' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161391385 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001161391385 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161391385/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161391385 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 872) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/872 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/872' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1c(O)cccc1Cl) `ZINC001161391385.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001161391385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161391385/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001161391385 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1c(O)cccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 12, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 3, 3, 3, 21, 21, 3, 21, 21, 21, 21, 21, 21, 3, 3, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 8, 10, 10, 10, 3, 3, 3, 21, 21, 3, 21, 3, 3, 3, 3, 20, 10, 10, 10] 100 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 92 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161391385 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161391385/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161391385 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 873) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/873 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/873' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1c(O)cccc1Cl) `ZINC001161391385.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001161391385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161391385/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001161391385 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1c(O)cccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 12, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 3, 3, 3, 21, 21, 3, 21, 21, 21, 21, 21, 21, 3, 3, 1, 1, 1, 1, 4, 4, 4, 11, 11, 11, 9, 11, 11, 11, 3, 3, 3, 21, 21, 3, 21, 3, 3, 3, 4, 22, 11, 11, 11] 100 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 96 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161391385 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001161391385 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161391385/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161391385/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161391385 Building ZINC001161391385 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161391385' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161391385 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001161391385 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161391385/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161391385 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 872) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/872: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1c(O)cccc1Cl) `ZINC001161391385.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001161391385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161391385/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001161391385 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1c(O)cccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 12, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 3, 3, 3, 21, 21, 3, 21, 21, 21, 21, 21, 21, 3, 3, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 8, 10, 10, 10, 3, 3, 3, 21, 21, 3, 21, 3, 3, 3, 3, 20, 10, 10, 10] 100 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 92 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161391385 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161391385/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161391385 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 873) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/873: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1c(O)cccc1Cl) `ZINC001161391385.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001161391385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161391385/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001161391385 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1c(O)cccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 12, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 3, 3, 3, 21, 21, 3, 21, 21, 21, 21, 21, 21, 3, 3, 1, 1, 1, 1, 4, 4, 4, 11, 11, 11, 9, 11, 11, 11, 3, 3, 3, 21, 21, 3, 21, 3, 3, 3, 4, 22, 11, 11, 11] 100 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 96 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161391385 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001161391385 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161391385/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161391385/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161391385 Building ZINC001161406764 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161406764' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161406764 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001161406764 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161406764/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161406764 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 874) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/874 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/874' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC(C2CCCCC2)C1) `ZINC001161406764.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001161406764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161406764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001161406764 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC(C2CCCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 14, 14, 3, 14, 14, 14, 14, 14, 14, 3, 3, 1, 1, 1, 1, 1, 2, 3, 3, 6, 10, 10, 10, 10, 10, 3, 3, 3, 3, 14, 14, 5, 14, 3, 3, 3, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3] 50 rigid atoms, others: [16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 65 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161406764 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161406764/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161406764 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 875) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/875 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/875' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC(C2CCCCC2)C1) `ZINC001161406764.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001161406764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161406764/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001161406764 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC(C2CCCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 15, 15, 3, 15, 15, 15, 15, 15, 15, 3, 3, 1, 1, 1, 1, 1, 2, 3, 3, 5, 8, 8, 8, 8, 8, 3, 3, 3, 3, 15, 15, 3, 15, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3] 50 rigid atoms, others: [16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 57 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161406764 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001161406764 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161406764/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161406764/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161406764 Building ZINC001161406764 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161406764' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161406764 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001161406764 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161406764/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161406764 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 874) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/874: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC(C2CCCCC2)C1) `ZINC001161406764.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001161406764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161406764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001161406764 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC(C2CCCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 14, 14, 3, 14, 14, 14, 14, 14, 14, 3, 3, 1, 1, 1, 1, 1, 2, 3, 3, 6, 10, 10, 10, 10, 10, 3, 3, 3, 3, 14, 14, 5, 14, 3, 3, 3, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3] 50 rigid atoms, others: [16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 65 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161406764 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161406764/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161406764 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 875) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/875: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC(C2CCCCC2)C1) `ZINC001161406764.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001161406764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161406764/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001161406764 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC(C2CCCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 15, 15, 3, 15, 15, 15, 15, 15, 15, 3, 3, 1, 1, 1, 1, 1, 2, 3, 3, 5, 8, 8, 8, 8, 8, 3, 3, 3, 3, 15, 15, 3, 15, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3] 50 rigid atoms, others: [16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 57 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161406764 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001161406764 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161406764/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161406764/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001161406764 Building ZINC001276410242 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276410242' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276410242 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001276410242 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276410242/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276410242 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 876) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/876 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/876' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc(Br)cc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1C) `ZINC001276410242.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001276410242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276410242/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001276410242 none COC(=O)c1cc(Br)cc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 17, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 11, 34, 11, 11, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 11, 11, 34, 34, 34, 11, 11, 4, 3, 1, 3, 11, 11, 11] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 91 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276410242 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276410242/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276410242 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 877) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/877 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/877' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc(Br)cc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1C) `ZINC001276410242.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001276410242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276410242/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001276410242 none COC(=O)c1cc(Br)cc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 17, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 11, 34, 11, 11, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 11, 11, 34, 34, 34, 11, 11, 4, 3, 1, 3, 11, 11, 11] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276410242 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001276410242 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276410242/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276410242/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276410242 Building ZINC001276410242 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276410242' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276410242 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001276410242 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276410242/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276410242 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 876) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/876: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc(Br)cc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1C) `ZINC001276410242.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001276410242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276410242/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001276410242 none COC(=O)c1cc(Br)cc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 17, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 11, 34, 11, 11, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 11, 11, 34, 34, 34, 11, 11, 4, 3, 1, 3, 11, 11, 11] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 91 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276410242 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276410242/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276410242 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 877) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/877: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc(Br)cc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1C) `ZINC001276410242.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001276410242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276410242/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001276410242 none COC(=O)c1cc(Br)cc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 17, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 11, 34, 11, 11, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 11, 11, 34, 34, 34, 11, 11, 4, 3, 1, 3, 11, 11, 11] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276410242 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001276410242 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276410242/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276410242/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276410242 Building ZINC001276578136 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276578136' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276578136 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001276578136 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276578136/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276578136 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 878) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/878 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/878' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2c(c1)C[C@H](C(C)C)CN2C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001276578136.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001276578136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276578136/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001276578136 none COc1ccc2c(c1)C[C@H](C(C)C)CN2C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 20, 20, 9, 8, 3, 8, 1, 1, 1, 3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 18, 18, 18, 9, 9, 9, 9, 9, 20, 20, 20, 20, 20, 20, 20, 9, 9, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 105 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276578136 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276578136/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276578136 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 879) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/879 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/879' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2c(c1)C[C@H](C(C)C)CN2C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001276578136.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001276578136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276578136/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001276578136 none COc1ccc2c(c1)C[C@H](C(C)C)CN2C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 18, 18, 9, 7, 3, 8, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 16, 16, 16, 9, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 18, 9, 9, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 97 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276578136 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001276578136 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276578136/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276578136/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276578136 Building ZINC001276578136 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276578136' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276578136 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001276578136 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276578136/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276578136 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 878) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/878: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2c(c1)C[C@H](C(C)C)CN2C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001276578136.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001276578136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276578136/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001276578136 none COc1ccc2c(c1)C[C@H](C(C)C)CN2C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 20, 20, 9, 8, 3, 8, 1, 1, 1, 3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 18, 18, 18, 9, 9, 9, 9, 9, 20, 20, 20, 20, 20, 20, 20, 9, 9, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 105 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276578136 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276578136/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276578136 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 879) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/879: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2c(c1)C[C@H](C(C)C)CN2C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001276578136.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001276578136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276578136/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001276578136 none COc1ccc2c(c1)C[C@H](C(C)C)CN2C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 18, 18, 9, 7, 3, 8, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 16, 16, 16, 9, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 18, 9, 9, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 97 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276578136 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001276578136 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276578136/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276578136/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276578136 Building ZINC001276578137 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276578137' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276578137 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001276578137 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276578137/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276578137 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 880) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/880 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/880' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2c(c1)C[C@@H](C(C)C)CN2C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001276578137.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001276578137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276578137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001276578137 none COc1ccc2c(c1)C[C@@H](C(C)C)CN2C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 17, 17, 9, 7, 3, 8, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 17, 17, 17, 9, 9, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 9, 9, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 87 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276578137 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276578137/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276578137 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 881) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/881 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/881' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2c(c1)C[C@@H](C(C)C)CN2C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001276578137.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001276578137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276578137/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001276578137 none COc1ccc2c(c1)C[C@@H](C(C)C)CN2C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 20, 20, 10, 8, 3, 9, 1, 1, 1, 3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 19, 19, 19, 10, 10, 10, 10, 10, 20, 20, 20, 20, 20, 20, 20, 10, 10, 3, 3, 3, 7, 7, 5, 7, 7, 3, 3, 3] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 109 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276578137 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001276578137 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276578137/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276578137/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276578137 Building ZINC001276578137 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276578137' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276578137 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001276578137 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276578137/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276578137 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 880) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/880: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2c(c1)C[C@@H](C(C)C)CN2C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001276578137.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001276578137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276578137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001276578137 none COc1ccc2c(c1)C[C@@H](C(C)C)CN2C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 17, 17, 9, 7, 3, 8, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 17, 17, 17, 9, 9, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 9, 9, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 87 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276578137 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276578137/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276578137 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 881) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/881: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2c(c1)C[C@@H](C(C)C)CN2C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001276578137.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001276578137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276578137/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001276578137 none COc1ccc2c(c1)C[C@@H](C(C)C)CN2C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 20, 20, 10, 8, 3, 9, 1, 1, 1, 3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 19, 19, 19, 10, 10, 10, 10, 10, 20, 20, 20, 20, 20, 20, 20, 10, 10, 3, 3, 3, 7, 7, 5, 7, 7, 3, 3, 3] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 109 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276578137 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001276578137 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276578137/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276578137/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276578137 Building ZINC001276620981 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276620981' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276620981 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001276620981 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276620981/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276620981 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 882) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/882 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/882' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC[C@H]1Cc1cccc(Br)c1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001276620981.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001276620981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276620981/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001276620981 none O=C(N1CCCC[C@H]1Cc1cccc(Br)c1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 17, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 8, 8, 8, 8, 8, 8, 8, 13, 27, 27, 27, 27, 27, 27, 1, 1, 1, 5, 5, 7, 7, 5, 7, 7, 7, 8, 8, 8, 8, 8, 8, 8, 8, 13, 13, 27, 27, 27, 27, 5, 7, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 89 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276620981 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276620981/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276620981 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 883) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/883 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/883' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC[C@H]1Cc1cccc(Br)c1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001276620981.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001276620981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276620981/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001276620981 none O=C(N1CCCC[C@H]1Cc1cccc(Br)c1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 17, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 6, 6, 6, 6, 6, 6, 11, 27, 27, 27, 27, 27, 27, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 27, 27, 27, 27, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 73 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276620981 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001276620981 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276620981/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276620981/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276620981 Building ZINC001276620981 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276620981' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276620981 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001276620981 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276620981/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276620981 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 882) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/882: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC[C@H]1Cc1cccc(Br)c1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001276620981.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001276620981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276620981/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001276620981 none O=C(N1CCCC[C@H]1Cc1cccc(Br)c1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 17, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 8, 8, 8, 8, 8, 8, 8, 13, 27, 27, 27, 27, 27, 27, 1, 1, 1, 5, 5, 7, 7, 5, 7, 7, 7, 8, 8, 8, 8, 8, 8, 8, 8, 13, 13, 27, 27, 27, 27, 5, 7, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 89 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276620981 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276620981/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276620981 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 883) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/883: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC[C@H]1Cc1cccc(Br)c1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001276620981.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001276620981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276620981/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001276620981 none O=C(N1CCCC[C@H]1Cc1cccc(Br)c1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 17, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 6, 6, 6, 6, 6, 6, 11, 27, 27, 27, 27, 27, 27, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 27, 27, 27, 27, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 73 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276620981 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001276620981 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276620981/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276620981/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276620981 Building ZINC001276620982 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276620982' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276620982 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001276620982 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276620982/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276620982 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 884) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/884 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/884' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC[C@@H]1Cc1cccc(Br)c1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001276620982.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001276620982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276620982/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001276620982 none O=C(N1CCCC[C@@H]1Cc1cccc(Br)c1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 17, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 6, 6, 6, 6, 6, 6, 12, 28, 28, 28, 28, 28, 28, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 28, 28, 28, 28, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 79 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276620982 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276620982/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276620982 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 885) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/885 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/885' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC[C@@H]1Cc1cccc(Br)c1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001276620982.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001276620982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276620982/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001276620982 none O=C(N1CCCC[C@@H]1Cc1cccc(Br)c1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 17, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 8, 8, 8, 8, 8, 8, 8, 13, 27, 27, 27, 27, 27, 27, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 13, 13, 27, 27, 27, 27, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 73 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276620982 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001276620982 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276620982/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276620982/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276620982 Building ZINC001276620982 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276620982' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276620982 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001276620982 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276620982/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276620982 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 884) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/884: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC[C@@H]1Cc1cccc(Br)c1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001276620982.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001276620982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276620982/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001276620982 none O=C(N1CCCC[C@@H]1Cc1cccc(Br)c1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 17, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 6, 6, 6, 6, 6, 6, 12, 28, 28, 28, 28, 28, 28, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 28, 28, 28, 28, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 79 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276620982 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276620982/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276620982 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 885) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/885: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC[C@@H]1Cc1cccc(Br)c1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001276620982.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001276620982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276620982/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001276620982 none O=C(N1CCCC[C@@H]1Cc1cccc(Br)c1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 17, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 8, 8, 8, 8, 8, 8, 8, 13, 27, 27, 27, 27, 27, 27, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 13, 13, 27, 27, 27, 27, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 73 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276620982 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001276620982 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276620982/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276620982/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276620982 Building ZINC001276706081 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276706081' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276706081 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001276706081 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276706081/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276706081 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 886) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/886 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/886' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)NC1(c2ccc(C)cc2Br)CCCCC1) `ZINC001276706081.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001276706081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276706081/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001276706081 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NC1(c2ccc(C)cc2Br)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Br', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 1, 1, 17, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 13, 30, 35, 35, 35, 35, 35, 35, 35, 30, 30, 30, 30, 30, 5, 5, 5, 5, 5, 5, 5, 7, 35, 35, 35, 35, 35, 35, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276706081 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276706081/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276706081 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 887) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/887 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/887' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC1(c2ccc(C)cc2Br)CCCCC1) `ZINC001276706081.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001276706081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276706081/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001276706081 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC1(c2ccc(C)cc2Br)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Br', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 1, 1, 17, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 3, 4, 4, 1, 1, 1, 1, 8, 8, 14, 31, 36, 36, 35, 36, 36, 36, 36, 31, 31, 31, 31, 31, 4, 4, 4, 4, 4, 4, 4, 8, 36, 36, 36, 36, 36, 36, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276706081 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001276706081 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276706081/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276706081/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276706081 Building ZINC001276706081 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276706081' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276706081 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001276706081 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276706081/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276706081 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 886) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/886: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)NC1(c2ccc(C)cc2Br)CCCCC1) `ZINC001276706081.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001276706081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276706081/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001276706081 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NC1(c2ccc(C)cc2Br)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Br', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 1, 1, 17, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 13, 30, 35, 35, 35, 35, 35, 35, 35, 30, 30, 30, 30, 30, 5, 5, 5, 5, 5, 5, 5, 7, 35, 35, 35, 35, 35, 35, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276706081 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276706081/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276706081 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 887) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/887: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC1(c2ccc(C)cc2Br)CCCCC1) `ZINC001276706081.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001276706081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276706081/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001276706081 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC1(c2ccc(C)cc2Br)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Br', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 1, 1, 17, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 3, 4, 4, 1, 1, 1, 1, 8, 8, 14, 31, 36, 36, 35, 36, 36, 36, 36, 31, 31, 31, 31, 31, 4, 4, 4, 4, 4, 4, 4, 8, 36, 36, 36, 36, 36, 36, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276706081 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001276706081 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276706081/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276706081/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001276706081 Building ZINC001277483360 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001277483360' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001277483360 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001277483360 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001277483360/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001277483360 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 888) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/888 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/888' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)ccc1C) `ZINC001277483360.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001277483360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001277483360/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001277483360 none CC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', '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, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 1, 5, 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, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 6, 6, 6, 6, 9, 9, 9, 6, 2, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001277483360 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001277483360/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001277483360 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 889) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/889 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/889' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)ccc1C) `ZINC001277483360.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001277483360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001277483360/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001277483360 none CC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', '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, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 1, 5, 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, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 5, 5, 5, 5, 8, 8, 8, 5, 2, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 5, 5, 5, 5, 5] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001277483360 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001277483360 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001277483360/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001277483360/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001277483360 Building ZINC001277483360 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001277483360' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001277483360 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001277483360 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001277483360/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001277483360 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 888) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/888: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)ccc1C) `ZINC001277483360.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001277483360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001277483360/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001277483360 none CC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', '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, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 1, 5, 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, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 6, 6, 6, 6, 9, 9, 9, 6, 2, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001277483360 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001277483360/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001277483360 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 889) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/889: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)ccc1C) `ZINC001277483360.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001277483360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001277483360/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001277483360 none CC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', '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, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 1, 5, 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, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 5, 5, 5, 5, 8, 8, 8, 5, 2, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 5, 5, 5, 5, 5] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001277483360 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001277483360 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001277483360/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001277483360/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001277483360 Building ZINC001277803562 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001277803562' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001277803562 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001277803562 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001277803562/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001277803562 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 890) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/890 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/890' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ncccc1C(=O)c1cccc(Cl)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001277803562.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001277803562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001277803562/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001277803562 none O=C(Nc1ncccc1C(=O)c1cccc(Cl)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 16, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 9, 9, 9, 9, 9, 9, 13, 13, 36, 36, 27, 36, 36, 36, 1, 1, 1, 8, 8, 8, 8, 8, 4, 9, 9, 9, 36, 36, 36, 36, 8, 8] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001277803562 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001277803562/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001277803562 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 891) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/891 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/891' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ncccc1C(=O)c1cccc(Cl)c1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001277803562.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001277803562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001277803562/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001277803562 none O=C(Nc1ncccc1C(=O)c1cccc(Cl)c1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 16, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 9, 9, 9, 9, 9, 9, 12, 12, 35, 35, 25, 35, 35, 35, 1, 1, 1, 8, 8, 8, 8, 8, 4, 9, 9, 9, 35, 35, 35, 35, 8, 8] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001277803562 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001277803562 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001277803562/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001277803562/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001277803562 Building ZINC001277803562 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001277803562' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001277803562 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001277803562 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001277803562/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001277803562 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 890) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/890: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ncccc1C(=O)c1cccc(Cl)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001277803562.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001277803562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001277803562/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001277803562 none O=C(Nc1ncccc1C(=O)c1cccc(Cl)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 16, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 9, 9, 9, 9, 9, 9, 13, 13, 36, 36, 27, 36, 36, 36, 1, 1, 1, 8, 8, 8, 8, 8, 4, 9, 9, 9, 36, 36, 36, 36, 8, 8] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001277803562 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001277803562/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001277803562 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 891) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/891: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ncccc1C(=O)c1cccc(Cl)c1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001277803562.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001277803562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001277803562/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001277803562 none O=C(Nc1ncccc1C(=O)c1cccc(Cl)c1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 16, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 9, 9, 9, 9, 9, 9, 12, 12, 35, 35, 25, 35, 35, 35, 1, 1, 1, 8, 8, 8, 8, 8, 4, 9, 9, 9, 35, 35, 35, 35, 8, 8] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001277803562 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001277803562 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001277803562/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001277803562/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001277803562 Building ZINC001278192658 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278192658' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278192658 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001278192658 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278192658/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278192658 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 892) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/892 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/892' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(F)cc(N(C)C)c1) `ZINC001278192658.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001278192658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278192658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001278192658 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(F)cc(N(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 15, 1, 1, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278192658 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278192658/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278192658 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 893) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/893 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/893' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(F)cc(N(C)C)c1) `ZINC001278192658.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001278192658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278192658/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001278192658 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(F)cc(N(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 15, 1, 1, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278192658 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001278192658 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278192658/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278192658/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278192658 Building ZINC001278192658 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278192658' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278192658 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001278192658 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278192658/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278192658 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 892) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/892: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(F)cc(N(C)C)c1) `ZINC001278192658.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001278192658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278192658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001278192658 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(F)cc(N(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 15, 1, 1, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278192658 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278192658/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278192658 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 893) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/893: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(F)cc(N(C)C)c1) `ZINC001278192658.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001278192658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278192658/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001278192658 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(F)cc(N(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 15, 1, 1, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278192658 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001278192658 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278192658/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278192658/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278192658 Building ZINC001278258850 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258850' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258850 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001278258850 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258850/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258850 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 894) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/894 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/894' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1CCNC(=O)OC(C)(C)C) `ZINC001278258850.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001278258850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258850/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001278258850 none C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1CCNC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 2, 6, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 6, 6, 6, 10, 13, 33, 44, 44, 48, 48, 48, 48, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 1, 3, 10, 10, 13, 13, 33, 48, 48, 48, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258850 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258850/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258850 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 895) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/895 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/895' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1CCNC(=O)OC(C)(C)C) `ZINC001278258850.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001278258850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258850/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001278258850 none C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1CCNC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 5, 2, 6, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 7, 7, 7, 10, 15, 29, 44, 44, 47, 47, 47, 47, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 1, 3, 10, 10, 15, 15, 29, 47, 47, 47, 47, 47, 47, 47, 47, 47] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258850 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001278258850 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258850/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258850/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258850 Building ZINC001278258850 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258850' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258850 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001278258850 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258850/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258850 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 894) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/894: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1CCNC(=O)OC(C)(C)C) `ZINC001278258850.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001278258850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258850/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001278258850 none C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1CCNC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 2, 6, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 6, 6, 6, 10, 13, 33, 44, 44, 48, 48, 48, 48, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 1, 3, 10, 10, 13, 13, 33, 48, 48, 48, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258850 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258850/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258850 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 895) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/895: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1CCNC(=O)OC(C)(C)C) `ZINC001278258850.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001278258850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258850/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001278258850 none C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1CCNC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 5, 2, 6, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 7, 7, 7, 10, 15, 29, 44, 44, 47, 47, 47, 47, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 1, 3, 10, 10, 15, 15, 29, 47, 47, 47, 47, 47, 47, 47, 47, 47] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258850 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001278258850 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258850/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258850/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258850 Building ZINC001278258851 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258851' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258851 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001278258851 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258851/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258851 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 896) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/896 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/896' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1CCNC(=O)OC(C)(C)C) `ZINC001278258851.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001278258851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258851/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001278258851 none C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1CCNC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 5, 5, 5, 11, 15, 33, 47, 47, 49, 49, 49, 49, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 1, 3, 11, 11, 15, 15, 33, 49, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258851 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258851/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258851 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 897) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/897 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/897' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1CCNC(=O)OC(C)(C)C) `ZINC001278258851.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001278258851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258851/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001278258851 none C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1CCNC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 6, 6, 6, 11, 16, 37, 48, 48, 50, 50, 50, 50, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 1, 2, 11, 11, 16, 16, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258851 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001278258851 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258851/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258851/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258851 Building ZINC001278258851 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258851' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258851 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001278258851 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258851/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258851 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 896) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/896: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1CCNC(=O)OC(C)(C)C) `ZINC001278258851.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001278258851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258851/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001278258851 none C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1CCNC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 5, 5, 5, 11, 15, 33, 47, 47, 49, 49, 49, 49, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 1, 3, 11, 11, 15, 15, 33, 49, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258851 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258851/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258851 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 897) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/897: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1CCNC(=O)OC(C)(C)C) `ZINC001278258851.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001278258851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258851/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001278258851 none C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1CCNC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 6, 6, 6, 11, 16, 37, 48, 48, 50, 50, 50, 50, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 1, 2, 11, 11, 16, 16, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258851 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001278258851 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258851/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258851/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258851 Building ZINC001278258852 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258852' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258852 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001278258852 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258852/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258852 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 898) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/898 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/898' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1CCNC(=O)OC(C)(C)C) `ZINC001278258852.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001278258852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258852/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001278258852 none C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1CCNC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 5, 1, 6, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 7, 7, 7, 10, 15, 29, 44, 44, 47, 47, 47, 47, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 1, 3, 10, 10, 15, 15, 29, 47, 47, 47, 47, 47, 47, 47, 47, 47] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258852 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258852/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258852 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 899) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/899 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/899' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1CCNC(=O)OC(C)(C)C) `ZINC001278258852.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001278258852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258852/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001278258852 none C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1CCNC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 5, 1, 6, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 6, 6, 6, 10, 13, 33, 43, 43, 49, 49, 49, 49, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 1, 3, 10, 10, 13, 13, 33, 49, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258852 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001278258852 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258852/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258852/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258852 Building ZINC001278258852 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258852' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258852 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001278258852 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258852/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258852 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 898) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/898: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1CCNC(=O)OC(C)(C)C) `ZINC001278258852.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001278258852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258852/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001278258852 none C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1CCNC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 5, 1, 6, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 7, 7, 7, 10, 15, 29, 44, 44, 47, 47, 47, 47, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 1, 3, 10, 10, 15, 15, 29, 47, 47, 47, 47, 47, 47, 47, 47, 47] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258852 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258852/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258852 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 899) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/899: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1CCNC(=O)OC(C)(C)C) `ZINC001278258852.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001278258852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258852/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001278258852 none C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1CCNC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 5, 1, 6, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 6, 6, 6, 10, 13, 33, 43, 43, 49, 49, 49, 49, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 1, 3, 10, 10, 13, 13, 33, 49, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258852 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001278258852 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258852/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258852/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258852 Building ZINC001278258853 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258853' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258853 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001278258853 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258853/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258853 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 900) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/900 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/900' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1CCNC(=O)OC(C)(C)C) `ZINC001278258853.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001278258853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258853/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001278258853 none C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1CCNC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 2, 5, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 7, 12, 33, 45, 45, 49, 49, 49, 49, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 3, 3, 7, 7, 12, 12, 33, 49, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 167 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258853 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258853/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258853 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 901) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/901 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/901' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1CCNC(=O)OC(C)(C)C) `ZINC001278258853.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001278258853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258853/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001278258853 none C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1CCNC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 3, 2, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 5, 5, 5, 12, 17, 31, 45, 45, 49, 49, 49, 49, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 1, 3, 12, 12, 17, 17, 31, 49, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258853 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001278258853 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258853/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258853/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258853 Building ZINC001278258853 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258853' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258853 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001278258853 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258853/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258853 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 900) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/900: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1CCNC(=O)OC(C)(C)C) `ZINC001278258853.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001278258853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258853/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001278258853 none C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1CCNC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 2, 5, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 7, 12, 33, 45, 45, 49, 49, 49, 49, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 3, 3, 7, 7, 12, 12, 33, 49, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 167 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258853 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258853/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258853 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 901) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/901: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1CCNC(=O)OC(C)(C)C) `ZINC001278258853.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001278258853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258853/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001278258853 none C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@@H]1CCNC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 3, 2, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 5, 5, 5, 12, 17, 31, 45, 45, 49, 49, 49, 49, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 1, 3, 12, 12, 17, 17, 31, 49, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258853 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001278258853 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258853/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258853/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278258853 Building ZINC001278610495 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278610495' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278610495 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001278610495 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278610495/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278610495 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 902) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/902 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/902' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]1(Cc2ccc(OC(F)(F)F)cc2)CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001278610495.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001278610495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278610495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001278610495 none C[C@]1(Cc2ccc(OC(F)(F)F)cc2)CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 9, 9, 9, 9, 9, 29, 30, 30, 30, 9, 9, 5, 5, 5, 2, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278610495 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278610495/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278610495 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 903) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/903 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/903' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]1(Cc2ccc(OC(F)(F)F)cc2)CCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001278610495.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001278610495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278610495/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001278610495 none C[C@]1(Cc2ccc(OC(F)(F)F)cc2)CCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 8, 8, 8, 8, 8, 30, 30, 30, 30, 8, 8, 4, 4, 4, 2, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278610495 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001278610495 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278610495/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278610495/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278610495 Building ZINC001278610495 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278610495' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278610495 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001278610495 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278610495/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278610495 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 902) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/902: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]1(Cc2ccc(OC(F)(F)F)cc2)CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001278610495.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001278610495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278610495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001278610495 none C[C@]1(Cc2ccc(OC(F)(F)F)cc2)CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 9, 9, 9, 9, 9, 29, 30, 30, 30, 9, 9, 5, 5, 5, 2, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278610495 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278610495/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278610495 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 903) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/903: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]1(Cc2ccc(OC(F)(F)F)cc2)CCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001278610495.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001278610495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278610495/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001278610495 none C[C@]1(Cc2ccc(OC(F)(F)F)cc2)CCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 8, 8, 8, 8, 8, 30, 30, 30, 30, 8, 8, 4, 4, 4, 2, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278610495 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001278610495 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278610495/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278610495/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278610495 Building ZINC001278610496 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278610496' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278610496 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001278610496 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278610496/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278610496 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 904) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/904 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/904' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(Cc2ccc(OC(F)(F)F)cc2)CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001278610496.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001278610496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278610496/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001278610496 none C[C@@]1(Cc2ccc(OC(F)(F)F)cc2)CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 8, 8, 8, 8, 8, 31, 31, 31, 31, 8, 8, 4, 4, 4, 2, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278610496 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278610496/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278610496 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 905) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/905 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/905' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(Cc2ccc(OC(F)(F)F)cc2)CCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001278610496.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001278610496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278610496/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001278610496 none C[C@@]1(Cc2ccc(OC(F)(F)F)cc2)CCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 9, 9, 9, 9, 9, 29, 30, 30, 30, 9, 9, 5, 5, 5, 2, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278610496 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001278610496 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278610496/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278610496/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278610496 Building ZINC001278610496 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278610496' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278610496 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001278610496 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278610496/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278610496 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 904) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/904: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(Cc2ccc(OC(F)(F)F)cc2)CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001278610496.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001278610496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278610496/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001278610496 none C[C@@]1(Cc2ccc(OC(F)(F)F)cc2)CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 8, 8, 8, 8, 8, 31, 31, 31, 31, 8, 8, 4, 4, 4, 2, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278610496 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278610496/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278610496 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 905) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/905: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(Cc2ccc(OC(F)(F)F)cc2)CCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001278610496.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001278610496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278610496/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001278610496 none C[C@@]1(Cc2ccc(OC(F)(F)F)cc2)CCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 9, 9, 9, 9, 9, 29, 30, 30, 30, 9, 9, 5, 5, 5, 2, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278610496 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001278610496 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278610496/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278610496/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001278610496 Building ZINC001264025152 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264025152' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264025152 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264025152 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264025152/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264025152 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 906) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/906 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/906' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(Oc2ccc(C(F)(F)F)cc2NC(=O)[C@]([O-])([SiH3])c2cnn(CC)c2)cc1) `ZINC001264025152.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264025152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264025152/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001264025152 none CCOc1ccc(Oc2ccc(C(F)(F)F)cc2NC(=O)[C@]([O-])([SiH3])c2cnn(CC)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 21, 14, 21, 21, 14, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 12, 6, 21, 21, 34, 34, 34, 34, 34, 21, 21, 4, 4, 4, 2, 6, 12, 12, 12, 12, 12, 6, 21, 21] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264025152 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264025152/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264025152 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 907) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/907 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/907' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(Oc2ccc(C(F)(F)F)cc2NC(=O)[C@@]([O-])([SiH3])c2cnn(CC)c2)cc1) `ZINC001264025152.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264025152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264025152/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001264025152 none CCOc1ccc(Oc2ccc(C(F)(F)F)cc2NC(=O)[C@@]([O-])([SiH3])c2cnn(CC)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 23, 14, 23, 23, 14, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 10, 6, 23, 23, 40, 40, 40, 40, 40, 23, 23, 4, 4, 4, 2, 6, 10, 10, 10, 10, 10, 6, 23, 23] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264025152 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264025152 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264025152/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264025152/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264025152 Building ZINC001264025152 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264025152' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264025152 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264025152 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264025152/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264025152 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 906) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/906: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(Oc2ccc(C(F)(F)F)cc2NC(=O)[C@]([O-])([SiH3])c2cnn(CC)c2)cc1) `ZINC001264025152.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264025152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264025152/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001264025152 none CCOc1ccc(Oc2ccc(C(F)(F)F)cc2NC(=O)[C@]([O-])([SiH3])c2cnn(CC)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 21, 14, 21, 21, 14, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 12, 6, 21, 21, 34, 34, 34, 34, 34, 21, 21, 4, 4, 4, 2, 6, 12, 12, 12, 12, 12, 6, 21, 21] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264025152 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264025152/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264025152 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 907) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/907: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(Oc2ccc(C(F)(F)F)cc2NC(=O)[C@@]([O-])([SiH3])c2cnn(CC)c2)cc1) `ZINC001264025152.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264025152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264025152/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001264025152 none CCOc1ccc(Oc2ccc(C(F)(F)F)cc2NC(=O)[C@@]([O-])([SiH3])c2cnn(CC)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 23, 14, 23, 23, 14, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 10, 6, 23, 23, 40, 40, 40, 40, 40, 23, 23, 4, 4, 4, 2, 6, 10, 10, 10, 10, 10, 6, 23, 23] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264025152 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264025152 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264025152/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264025152/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264025152 Building ZINC001264057588 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264057588' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264057588 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264057588 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264057588/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264057588 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 908) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/908 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/908' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C(=O)c2c(NC(=O)[C@]([O-])([SiH3])c3ccc(C)cc3)sc3c2CCCC3)cc1) `ZINC001264057588.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264057588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264057588/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001264057588 none COc1ccc(C(=O)c2c(NC(=O)[C@]([O-])([SiH3])c3ccc(C)cc3)sc3c2CCCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 14, 1, 1, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 29, 43, 29, 6, 6, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 29, 29, 29, 29, 29, 29, 29, 49, 49, 49, 49, 49, 49, 49, 6, 5, 5, 5, 5, 5, 5, 5, 29, 29, 29, 29, 29, 29, 29, 29, 49, 49] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264057588 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264057588/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264057588 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 909) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/909 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/909' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C(=O)c2c(NC(=O)[C@@]([O-])([SiH3])c3ccc(C)cc3)sc3c2CCCC3)cc1) `ZINC001264057588.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264057588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264057588/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001264057588 none COc1ccc(C(=O)c2c(NC(=O)[C@@]([O-])([SiH3])c3ccc(C)cc3)sc3c2CCCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 14, 1, 1, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 42, 42, 48, 48, 42, 26, 42, 26, 6, 6, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 26, 26, 26, 26, 26, 26, 26, 48, 48, 48, 48, 48, 48, 48, 6, 4, 4, 4, 4, 4, 4, 4, 26, 26, 26, 26, 26, 26, 26, 26, 48, 48] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264057588 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264057588 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264057588/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264057588/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264057588 Building ZINC001264057588 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264057588' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264057588 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264057588 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264057588/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264057588 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 908) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/908: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C(=O)c2c(NC(=O)[C@]([O-])([SiH3])c3ccc(C)cc3)sc3c2CCCC3)cc1) `ZINC001264057588.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264057588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264057588/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001264057588 none COc1ccc(C(=O)c2c(NC(=O)[C@]([O-])([SiH3])c3ccc(C)cc3)sc3c2CCCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 14, 1, 1, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 29, 43, 29, 6, 6, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 29, 29, 29, 29, 29, 29, 29, 49, 49, 49, 49, 49, 49, 49, 6, 5, 5, 5, 5, 5, 5, 5, 29, 29, 29, 29, 29, 29, 29, 29, 49, 49] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264057588 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264057588/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264057588 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 909) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/909: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C(=O)c2c(NC(=O)[C@@]([O-])([SiH3])c3ccc(C)cc3)sc3c2CCCC3)cc1) `ZINC001264057588.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264057588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264057588/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001264057588 none COc1ccc(C(=O)c2c(NC(=O)[C@@]([O-])([SiH3])c3ccc(C)cc3)sc3c2CCCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 14, 1, 1, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 42, 42, 48, 48, 42, 26, 42, 26, 6, 6, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 26, 26, 26, 26, 26, 26, 26, 48, 48, 48, 48, 48, 48, 48, 6, 4, 4, 4, 4, 4, 4, 4, 26, 26, 26, 26, 26, 26, 26, 26, 48, 48] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264057588 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264057588 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264057588/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264057588/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264057588 Building ZINC001264068601 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264068601' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264068601 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264068601 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264068601/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264068601 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 910) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/910 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/910' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1c2ccccc2C[C@H]1C) `ZINC001264068601.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264068601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264068601/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001264068601 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1c2ccccc2C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 25, 25, 5, 25, 25, 25, 25, 25, 25, 5, 5, 1, 1, 1, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 5, 25, 25, 5, 25, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 75 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264068601 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264068601/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264068601 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 911) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/911 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/911' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1c2ccccc2C[C@H]1C) `ZINC001264068601.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264068601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264068601/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001264068601 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1c2ccccc2C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 33, 33, 9, 33, 33, 33, 33, 33, 33, 4, 4, 1, 1, 1, 2, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 4, 33, 33, 11, 33, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 86 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264068601 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264068601 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264068601/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264068601/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264068601 Building ZINC001264068601 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264068601' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264068601 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264068601 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264068601/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264068601 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 910) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/910: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1c2ccccc2C[C@H]1C) `ZINC001264068601.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264068601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264068601/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001264068601 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1c2ccccc2C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 25, 25, 5, 25, 25, 25, 25, 25, 25, 5, 5, 1, 1, 1, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 5, 25, 25, 5, 25, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 75 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264068601 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264068601/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264068601 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 911) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/911: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1c2ccccc2C[C@H]1C) `ZINC001264068601.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264068601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264068601/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001264068601 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1c2ccccc2C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 33, 33, 9, 33, 33, 33, 33, 33, 33, 4, 4, 1, 1, 1, 2, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 4, 33, 33, 11, 33, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 86 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264068601 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264068601 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264068601/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264068601/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264068601 Building ZINC001264068602 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264068602' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264068602 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264068602 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264068602/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264068602 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 912) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/912 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/912' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1c2ccccc2C[C@@H]1C) `ZINC001264068602.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264068602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264068602/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001264068602 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1c2ccccc2C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 30, 30, 5, 30, 30, 30, 30, 30, 30, 5, 5, 1, 1, 1, 2, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 5, 5, 30, 30, 5, 30, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 87 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264068602 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264068602/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264068602 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 913) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/913 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/913' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1c2ccccc2C[C@@H]1C) `ZINC001264068602.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264068602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264068602/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001264068602 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1c2ccccc2C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 26, 26, 4, 26, 26, 26, 26, 26, 26, 4, 4, 1, 1, 1, 2, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 4, 26, 26, 4, 26, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 77 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264068602 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264068602 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264068602/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264068602/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264068602 Building ZINC001264068602 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264068602' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264068602 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264068602 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264068602/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264068602 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 912) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/912: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1c2ccccc2C[C@@H]1C) `ZINC001264068602.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264068602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264068602/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001264068602 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1c2ccccc2C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 30, 30, 5, 30, 30, 30, 30, 30, 30, 5, 5, 1, 1, 1, 2, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 5, 5, 30, 30, 5, 30, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 87 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264068602 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264068602/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264068602 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 913) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/913: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1c2ccccc2C[C@@H]1C) `ZINC001264068602.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264068602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264068602/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001264068602 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1c2ccccc2C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 26, 26, 4, 26, 26, 26, 26, 26, 26, 4, 4, 1, 1, 1, 2, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 4, 26, 26, 4, 26, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 77 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264068602 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264068602 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264068602/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264068602/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264068602 Building ZINC001264129969 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264129969' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264129969 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264129969 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264129969/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264129969 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 914) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/914 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/914' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2nc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)sc2C)cc1) `ZINC001264129969.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264129969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264129969/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001264129969 none COc1ccc(c2nc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)sc2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'S.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 14, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 16, 8, 31, 31, 8, 8, 8, 4, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 8, 8, 8, 31, 31, 31, 31, 31, 31, 31, 4, 10, 10, 8, 8, 8, 31, 31] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264129969 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264129969/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264129969 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 915) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/915 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/915' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2nc(NC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)sc2C)cc1) `ZINC001264129969.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264129969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264129969/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001264129969 none COc1ccc(c2nc(NC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)sc2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'S.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 14, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 16, 16, 31, 31, 8, 8, 8, 4, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 8, 8, 8, 31, 31, 31, 31, 31, 31, 31, 4, 10, 10, 8, 8, 8, 31, 31] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264129969 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264129969 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264129969/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264129969/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264129969 Building ZINC001264129969 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264129969' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264129969 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264129969 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264129969/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264129969 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 914) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/914: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2nc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)sc2C)cc1) `ZINC001264129969.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264129969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264129969/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001264129969 none COc1ccc(c2nc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)sc2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'S.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 14, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 16, 8, 31, 31, 8, 8, 8, 4, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 8, 8, 8, 31, 31, 31, 31, 31, 31, 31, 4, 10, 10, 8, 8, 8, 31, 31] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264129969 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264129969/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264129969 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 915) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/915: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2nc(NC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)sc2C)cc1) `ZINC001264129969.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264129969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264129969/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001264129969 none COc1ccc(c2nc(NC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)sc2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'S.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 14, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 16, 16, 31, 31, 8, 8, 8, 4, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 8, 8, 8, 31, 31, 31, 31, 31, 31, 31, 4, 10, 10, 8, 8, 8, 31, 31] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264129969 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264129969 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264129969/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264129969/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264129969 Building ZINC001264142758 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264142758' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264142758 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264142758 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264142758/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264142758 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 916) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/916 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/916' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc2ccc(Br)cc2s1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001264142758.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264142758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264142758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 30 natoms 29 natoms 28 natoms 27 names: ZINC001264142758 none O=C(Nc1nc2ccc(Br)cc2s1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 17, 1, 1, 14, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 11, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 12, 12, 12, 12, 12, 11, 21, 21, 21, 12, 12] 42 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 55 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264142758 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264142758/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264142758 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 917) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/917 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/917' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc2ccc(Br)cc2s1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001264142758.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264142758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264142758/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 30 natoms 29 natoms 28 natoms 27 names: ZINC001264142758 none O=C(Nc1nc2ccc(Br)cc2s1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 17, 1, 1, 14, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 11, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 12, 12, 12, 12, 12, 11, 21, 21, 21, 12, 12] 42 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 55 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264142758 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264142758 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264142758/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264142758/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264142758 Building ZINC001264142758 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264142758' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264142758 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264142758 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264142758/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264142758 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 916) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/916: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc2ccc(Br)cc2s1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001264142758.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264142758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264142758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 30 natoms 29 natoms 28 natoms 27 names: ZINC001264142758 none O=C(Nc1nc2ccc(Br)cc2s1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 17, 1, 1, 14, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 11, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 12, 12, 12, 12, 12, 11, 21, 21, 21, 12, 12] 42 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 55 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264142758 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264142758/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264142758 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 917) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/917: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc2ccc(Br)cc2s1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001264142758.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264142758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264142758/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 30 natoms 29 natoms 28 natoms 27 names: ZINC001264142758 none O=C(Nc1nc2ccc(Br)cc2s1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 17, 1, 1, 14, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 11, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 12, 12, 12, 12, 12, 11, 21, 21, 21, 12, 12] 42 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 55 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264142758 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264142758 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264142758/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264142758/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264142758 Building ZINC001264171695 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264171695' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264171695 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264171695 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264171695/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264171695 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 918) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/918 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/918' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)c1cc(F)c(Cl)cc1Cl) `ZINC001264171695.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264171695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264171695/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001264171695 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)c1cc(F)c(Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 15, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 9, 9, 4, 9, 9, 4, 4, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 36, 36, 36, 36, 36, 36, 36, 36, 4, 4, 4, 9, 9, 4, 9, 9, 4, 4, 4, 6, 12, 12, 12, 36, 36] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 110 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264171695 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264171695/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264171695 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 919) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/919 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/919' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)c1cc(F)c(Cl)cc1Cl) `ZINC001264171695.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264171695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264171695/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001264171695 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)c1cc(F)c(Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 15, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 8, 8, 5, 8, 8, 4, 4, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 35, 35, 35, 35, 35, 35, 35, 35, 4, 4, 4, 8, 8, 8, 8, 8, 4, 4, 4, 6, 12, 12, 12, 35, 35] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 111 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264171695 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264171695 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264171695/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264171695/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264171695 Building ZINC001264171695 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264171695' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264171695 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264171695 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264171695/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264171695 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 918) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/918: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)c1cc(F)c(Cl)cc1Cl) `ZINC001264171695.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264171695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264171695/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001264171695 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)c1cc(F)c(Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 15, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 9, 9, 4, 9, 9, 4, 4, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 36, 36, 36, 36, 36, 36, 36, 36, 4, 4, 4, 9, 9, 4, 9, 9, 4, 4, 4, 6, 12, 12, 12, 36, 36] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 110 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264171695 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264171695/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264171695 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 919) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/919: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)c1cc(F)c(Cl)cc1Cl) `ZINC001264171695.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264171695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264171695/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001264171695 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)c1cc(F)c(Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 15, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 8, 8, 5, 8, 8, 4, 4, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 35, 35, 35, 35, 35, 35, 35, 35, 4, 4, 4, 8, 8, 8, 8, 8, 4, 4, 4, 6, 12, 12, 12, 35, 35] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 111 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264171695 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264171695 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264171695/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264171695/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264171695 Building ZINC001264171696 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264171696' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264171696 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264171696 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264171696/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264171696 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 920) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/920 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/920' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)c1cc(F)c(Cl)cc1Cl) `ZINC001264171696.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264171696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264171696/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001264171696 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)c1cc(F)c(Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 15, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 36, 36, 36, 36, 36, 36, 36, 36, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4, 6, 13, 13, 13, 36, 36] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 111 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264171696 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264171696/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264171696 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 921) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/921 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/921' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)c1cc(F)c(Cl)cc1Cl) `ZINC001264171696.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264171696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264171696/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001264171696 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)c1cc(F)c(Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 15, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 10, 10, 6, 10, 10, 4, 4, 1, 1, 1, 1, 7, 7, 7, 13, 13, 13, 36, 36, 36, 36, 36, 36, 36, 36, 4, 4, 4, 10, 10, 8, 10, 10, 4, 4, 4, 7, 13, 13, 13, 36, 36] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 111 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264171696 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264171696 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264171696/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264171696/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264171696 Building ZINC001264171696 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264171696' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264171696 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264171696 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264171696/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264171696 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 920) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/920: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)c1cc(F)c(Cl)cc1Cl) `ZINC001264171696.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264171696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264171696/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001264171696 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)c1cc(F)c(Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 15, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 36, 36, 36, 36, 36, 36, 36, 36, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4, 6, 13, 13, 13, 36, 36] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 111 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264171696 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264171696/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264171696 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 921) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/921: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)c1cc(F)c(Cl)cc1Cl) `ZINC001264171696.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264171696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264171696/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001264171696 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)c1cc(F)c(Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 15, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 10, 10, 6, 10, 10, 4, 4, 1, 1, 1, 1, 7, 7, 7, 13, 13, 13, 36, 36, 36, 36, 36, 36, 36, 36, 4, 4, 4, 10, 10, 8, 10, 10, 4, 4, 4, 7, 13, 13, 13, 36, 36] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 111 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264171696 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264171696 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264171696/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264171696/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264171696 Building ZINC001264173590 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264173590' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264173590 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264173590 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264173590/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264173590 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 922) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/922 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/922' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(c2nnc3n2CCCCC3)cc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001264173590.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264173590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264173590/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001264173590 none O=C(Nc1ccc(c2nnc3n2CCCCC3)cc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 8, 1, 8, 5, 5, 5, 5, 5, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 9, 9, 4, 10, 29, 46, 46, 29, 46, 46, 46, 46, 46, 9, 9, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 9, 9, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 9, 9, 3, 1, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264173590 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264173590/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264173590 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 923) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/923 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/923' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(c2nnc3n2CCCCC3)cc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001264173590.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264173590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264173590/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001264173590 none O=C(Nc1ccc(c2nnc3n2CCCCC3)cc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 8, 1, 8, 5, 5, 5, 5, 5, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 9, 9, 4, 9, 29, 44, 44, 30, 44, 44, 44, 44, 44, 9, 9, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 9, 9, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 9, 9, 3, 1, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264173590 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264173590 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264173590/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264173590/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264173590 Building ZINC001264173590 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264173590' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264173590 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264173590 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264173590/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264173590 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 922) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/922: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(c2nnc3n2CCCCC3)cc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001264173590.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264173590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264173590/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001264173590 none O=C(Nc1ccc(c2nnc3n2CCCCC3)cc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 8, 1, 8, 5, 5, 5, 5, 5, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 9, 9, 4, 10, 29, 46, 46, 29, 46, 46, 46, 46, 46, 9, 9, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 9, 9, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 9, 9, 3, 1, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264173590 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264173590/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264173590 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 923) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/923: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(c2nnc3n2CCCCC3)cc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001264173590.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264173590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264173590/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001264173590 none O=C(Nc1ccc(c2nnc3n2CCCCC3)cc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 8, 1, 8, 5, 5, 5, 5, 5, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 9, 9, 4, 9, 29, 44, 44, 30, 44, 44, 44, 44, 44, 9, 9, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 9, 9, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 9, 9, 3, 1, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264173590 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264173590 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264173590/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264173590/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264173590 Building ZINC001264213682 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264213682' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264213682 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264213682 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264213682/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264213682 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 924) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/924 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/924' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)CCc1ccccc1) `ZINC001264213682.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264213682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264213682/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001264213682 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)CCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 11, 12, 12, 12, 12, 12, 12, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2, 3, 7, 7, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 79 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264213682 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264213682/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264213682 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 925) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/925 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/925' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)CCc1ccccc1) `ZINC001264213682.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264213682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264213682/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001264213682 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)CCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 13, 13, 2, 13, 13, 13, 13, 13, 13, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 13, 14, 14, 14, 14, 14, 14, 2, 2, 2, 13, 13, 2, 13, 2, 2, 2, 2, 7, 7, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 94 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264213682 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264213682 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264213682/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264213682/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264213682 Building ZINC001264213682 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264213682' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264213682 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264213682 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264213682/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264213682 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 924) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/924: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)CCc1ccccc1) `ZINC001264213682.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264213682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264213682/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001264213682 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)CCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 11, 12, 12, 12, 12, 12, 12, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2, 3, 7, 7, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 79 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264213682 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264213682/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264213682 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 925) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/925: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)CCc1ccccc1) `ZINC001264213682.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264213682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264213682/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001264213682 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)CCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 13, 13, 2, 13, 13, 13, 13, 13, 13, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 13, 14, 14, 14, 14, 14, 14, 2, 2, 2, 13, 13, 2, 13, 2, 2, 2, 2, 7, 7, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 94 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264213682 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264213682 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264213682/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264213682/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264213682 Building ZINC001264213683 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264213683' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264213683 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264213683 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264213683/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264213683 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 926) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/926 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/926' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)CCc1ccccc1) `ZINC001264213683.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264213683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264213683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001264213683 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)CCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 14, 14, 3, 14, 14, 14, 14, 14, 14, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 13, 14, 14, 14, 14, 14, 14, 3, 3, 3, 14, 14, 3, 14, 3, 3, 3, 2, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 98 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264213683 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264213683/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264213683 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 927) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/927 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/927' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)CCc1ccccc1) `ZINC001264213683.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264213683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264213683/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001264213683 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)CCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 11, 12, 12, 12, 12, 12, 12, 2, 2, 2, 10, 10, 3, 10, 2, 2, 2, 3, 7, 7, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 81 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264213683 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264213683 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264213683/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264213683/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264213683 Building ZINC001264213683 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264213683' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264213683 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264213683 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264213683/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264213683 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 926) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/926: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)CCc1ccccc1) `ZINC001264213683.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264213683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264213683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001264213683 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)CCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 14, 14, 3, 14, 14, 14, 14, 14, 14, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 13, 14, 14, 14, 14, 14, 14, 3, 3, 3, 14, 14, 3, 14, 3, 3, 3, 2, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 98 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264213683 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264213683/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264213683 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 927) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/927: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)CCc1ccccc1) `ZINC001264213683.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264213683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264213683/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001264213683 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)CCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 11, 12, 12, 12, 12, 12, 12, 2, 2, 2, 10, 10, 3, 10, 2, 2, 2, 3, 7, 7, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 81 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264213683 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264213683 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264213683/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264213683/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264213683 Building ZINC001264216107 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264216107' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264216107 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264216107 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264216107/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264216107 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 928) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/928 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/928' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1OCCC) `ZINC001264216107.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264216107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264216107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001264216107 none CCCOc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1OCCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 11, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 2, 10, 13, 21, 22, 22, 22, 22, 22, 12, 12, 2, 2, 1, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 13, 13, 21, 21, 21, 21, 21] 50 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 41] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264216107 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264216107/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264216107 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 929) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/929 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/929' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1OCCC) `ZINC001264216107.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264216107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264216107/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001264216107 none CCCOc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1OCCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 10, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 2, 10, 12, 22, 22, 22, 22, 22, 22, 12, 12, 2, 2, 1, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 12, 12, 22, 22, 22, 22, 22] 50 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 41] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264216107 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264216107 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264216107/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264216107/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264216107 Building ZINC001264216107 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264216107' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264216107 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264216107 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264216107/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264216107 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 928) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/928: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1OCCC) `ZINC001264216107.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264216107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264216107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001264216107 none CCCOc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1OCCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 11, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 2, 10, 13, 21, 22, 22, 22, 22, 22, 12, 12, 2, 2, 1, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 13, 13, 21, 21, 21, 21, 21] 50 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 41] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264216107 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264216107/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264216107 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 929) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/929: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1OCCC) `ZINC001264216107.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264216107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264216107/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001264216107 none CCCOc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1OCCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 10, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 2, 10, 12, 22, 22, 22, 22, 22, 22, 12, 12, 2, 2, 1, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 12, 12, 22, 22, 22, 22, 22] 50 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 41] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264216107 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264216107 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264216107/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264216107/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264216107 Building ZINC001264236884 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264236884' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264236884 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264236884 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264236884/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264236884 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 930) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/930 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/930' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](c2c[nH]c3ccccc32)c2ccccc2)cc1Cl) `ZINC001264236884.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264236884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264236884/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001264236884 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](c2c[nH]c3ccccc32)c2ccccc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 9, 13, 13, 25, 25, 25, 25, 25, 25, 25, 25, 25, 13, 15, 15, 13, 15, 15, 4, 4, 4, 8, 8, 8, 4, 4, 2, 9, 9, 25, 25, 25, 25, 25, 15, 15, 13, 15, 15, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264236884 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264236884/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264236884 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 931) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/931 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/931' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](c2c[nH]c3ccccc32)c2ccccc2)cc1Cl) `ZINC001264236884.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264236884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264236884/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001264236884 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](c2c[nH]c3ccccc32)c2ccccc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 2, 5, 5, 1, 1, 1, 1, 2, 2, 2, 10, 16, 16, 23, 23, 23, 23, 23, 23, 23, 23, 23, 16, 18, 18, 18, 18, 18, 5, 5, 5, 10, 10, 10, 5, 5, 2, 10, 10, 23, 23, 23, 23, 23, 18, 18, 18, 18, 18, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264236884 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264236884 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264236884/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264236884/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264236884 Building ZINC001264236884 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264236884' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264236884 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264236884 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264236884/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264236884 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 930) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/930: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](c2c[nH]c3ccccc32)c2ccccc2)cc1Cl) `ZINC001264236884.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264236884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264236884/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001264236884 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](c2c[nH]c3ccccc32)c2ccccc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 9, 13, 13, 25, 25, 25, 25, 25, 25, 25, 25, 25, 13, 15, 15, 13, 15, 15, 4, 4, 4, 8, 8, 8, 4, 4, 2, 9, 9, 25, 25, 25, 25, 25, 15, 15, 13, 15, 15, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264236884 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264236884/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264236884 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 931) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/931: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](c2c[nH]c3ccccc32)c2ccccc2)cc1Cl) `ZINC001264236884.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264236884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264236884/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001264236884 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](c2c[nH]c3ccccc32)c2ccccc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 2, 5, 5, 1, 1, 1, 1, 2, 2, 2, 10, 16, 16, 23, 23, 23, 23, 23, 23, 23, 23, 23, 16, 18, 18, 18, 18, 18, 5, 5, 5, 10, 10, 10, 5, 5, 2, 10, 10, 23, 23, 23, 23, 23, 18, 18, 18, 18, 18, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264236884 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264236884 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264236884/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264236884/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264236884 Building ZINC001264236885 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264236885' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264236885 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264236885 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264236885/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264236885 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 932) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/932 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/932' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](c2c[nH]c3ccccc32)c2ccccc2)cc1Cl) `ZINC001264236885.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264236885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264236885/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001264236885 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](c2c[nH]c3ccccc32)c2ccccc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 2, 5, 5, 1, 1, 1, 1, 2, 2, 2, 10, 16, 16, 23, 23, 23, 23, 23, 23, 23, 23, 23, 16, 18, 18, 16, 18, 18, 5, 5, 5, 10, 10, 10, 5, 5, 2, 10, 10, 23, 23, 23, 23, 23, 18, 18, 16, 18, 18, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264236885 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264236885/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264236885 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 933) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/933 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/933' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](c2c[nH]c3ccccc32)c2ccccc2)cc1Cl) `ZINC001264236885.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264236885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264236885/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001264236885 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](c2c[nH]c3ccccc32)c2ccccc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 9, 13, 13, 25, 25, 25, 25, 25, 25, 25, 25, 25, 13, 15, 15, 13, 15, 15, 4, 4, 4, 8, 8, 8, 4, 4, 2, 9, 9, 25, 25, 25, 25, 25, 15, 15, 13, 15, 15, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264236885 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264236885 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264236885/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264236885/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264236885 Building ZINC001264236885 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264236885' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264236885 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264236885 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264236885/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264236885 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 932) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/932: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](c2c[nH]c3ccccc32)c2ccccc2)cc1Cl) `ZINC001264236885.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264236885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264236885/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001264236885 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](c2c[nH]c3ccccc32)c2ccccc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 2, 5, 5, 1, 1, 1, 1, 2, 2, 2, 10, 16, 16, 23, 23, 23, 23, 23, 23, 23, 23, 23, 16, 18, 18, 16, 18, 18, 5, 5, 5, 10, 10, 10, 5, 5, 2, 10, 10, 23, 23, 23, 23, 23, 18, 18, 16, 18, 18, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264236885 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264236885/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264236885 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 933) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/933: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](c2c[nH]c3ccccc32)c2ccccc2)cc1Cl) `ZINC001264236885.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264236885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264236885/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001264236885 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](c2c[nH]c3ccccc32)c2ccccc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 9, 13, 13, 25, 25, 25, 25, 25, 25, 25, 25, 25, 13, 15, 15, 13, 15, 15, 4, 4, 4, 8, 8, 8, 4, 4, 2, 9, 9, 25, 25, 25, 25, 25, 15, 15, 13, 15, 15, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264236885 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264236885 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264236885/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264236885/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264236885 Building ZINC001264245163 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264245163' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264245163 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264245163 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264245163/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264245163 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 934) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/934 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/934' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1cccc(C(=O)Nc2cccc(C(F)(F)F)c2)c1) `ZINC001264245163.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264245163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264245163/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001264245163 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1cccc(C(=O)Nc2cccc(C(F)(F)F)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 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: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 10, 10, 14, 14, 14, 50, 50, 17, 50, 50, 50, 50, 50, 50, 10, 2, 2, 2, 2, 2, 2, 2, 4, 10, 10, 10, 14, 50, 50, 23, 50, 10] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264245163 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264245163/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264245163 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 935) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/935 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/935' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1cccc(C(=O)Nc2cccc(C(F)(F)F)c2)c1) `ZINC001264245163.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264245163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264245163/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001264245163 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1cccc(C(=O)Nc2cccc(C(F)(F)F)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 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: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 10, 10, 14, 14, 14, 50, 50, 14, 50, 50, 50, 50, 50, 50, 10, 2, 2, 2, 2, 2, 2, 2, 4, 10, 10, 10, 14, 50, 50, 23, 50, 10] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264245163 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264245163 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264245163/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264245163/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264245163 Building ZINC001264245163 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264245163' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264245163 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264245163 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264245163/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264245163 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 934) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/934: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1cccc(C(=O)Nc2cccc(C(F)(F)F)c2)c1) `ZINC001264245163.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264245163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264245163/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001264245163 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1cccc(C(=O)Nc2cccc(C(F)(F)F)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 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: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 10, 10, 14, 14, 14, 50, 50, 17, 50, 50, 50, 50, 50, 50, 10, 2, 2, 2, 2, 2, 2, 2, 4, 10, 10, 10, 14, 50, 50, 23, 50, 10] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264245163 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264245163/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264245163 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 935) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/935: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1cccc(C(=O)Nc2cccc(C(F)(F)F)c2)c1) `ZINC001264245163.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264245163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264245163/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001264245163 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1cccc(C(=O)Nc2cccc(C(F)(F)F)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 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: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 10, 10, 14, 14, 14, 50, 50, 14, 50, 50, 50, 50, 50, 50, 10, 2, 2, 2, 2, 2, 2, 2, 4, 10, 10, 10, 14, 50, 50, 23, 50, 10] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264245163 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264245163 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264245163/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264245163/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264245163 Building ZINC001264262428 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264262428' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264262428 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264262428 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264262428/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264262428 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 936) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/936 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/936' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(N(Cc2ccccc2)C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1) `ZINC001264262428.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264262428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264262428/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001264262428 none COc1ccc(N(Cc2ccccc2)C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 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: [22, 13, 9, 22, 22, 9, 5, 9, 20, 23, 23, 20, 23, 23, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 22, 22, 22, 22, 22, 22, 22, 20, 20, 23, 23, 20, 23, 23, 6, 6, 22, 22] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264262428 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264262428/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264262428 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 937) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/937 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/937' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(N(Cc2ccccc2)C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1) `ZINC001264262428.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264262428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264262428/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001264262428 none COc1ccc(N(Cc2ccccc2)C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 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: [19, 19, 18, 19, 19, 9, 5, 9, 18, 21, 21, 21, 21, 21, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 19, 19, 19, 19, 19, 19, 19, 18, 18, 21, 21, 21, 21, 21, 6, 6, 19, 19] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264262428 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264262428 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264262428/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264262428/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264262428 Building ZINC001264262428 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264262428' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264262428 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264262428 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264262428/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264262428 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 936) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/936: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(N(Cc2ccccc2)C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1) `ZINC001264262428.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264262428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264262428/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001264262428 none COc1ccc(N(Cc2ccccc2)C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 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: [22, 13, 9, 22, 22, 9, 5, 9, 20, 23, 23, 20, 23, 23, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 22, 22, 22, 22, 22, 22, 22, 20, 20, 23, 23, 20, 23, 23, 6, 6, 22, 22] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264262428 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264262428/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264262428 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 937) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/937: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(N(Cc2ccccc2)C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1) `ZINC001264262428.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264262428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264262428/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001264262428 none COc1ccc(N(Cc2ccccc2)C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 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: [19, 19, 18, 19, 19, 9, 5, 9, 18, 21, 21, 21, 21, 21, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 19, 19, 19, 19, 19, 19, 19, 18, 18, 21, 21, 21, 21, 21, 6, 6, 19, 19] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264262428 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264262428 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264262428/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264262428/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264262428 Building ZINC001264264154 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264264154' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264264154 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264264154 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264264154/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264264154 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 938) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/938 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/938' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(Cc2ccc(c3ccccc3F)s2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001264264154.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264264154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264264154/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001264264154 none O=C(N1CCN(Cc2ccc(c3ccccc3F)s2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'S.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 14, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 6, 6, 6, 6, 12, 21, 21, 21, 21, 50, 50, 37, 50, 50, 50, 21, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 12, 12, 21, 21, 50, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1] 50 rigid atoms, others: [1, 46, 47, 48, 49, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264264154 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264264154/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264264154 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 939) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/939 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/939' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(Cc2ccc(c3ccccc3F)s2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001264264154.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264264154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264264154/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001264264154 none O=C(N1CCN(Cc2ccc(c3ccccc3F)s2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'S.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 14, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 4, 4, 4, 4, 11, 22, 22, 22, 22, 50, 50, 29, 50, 50, 50, 22, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 11, 11, 22, 22, 50, 50, 50, 50, 4, 4, 4, 4, 1, 1, 1, 1] 50 rigid atoms, others: [1, 46, 47, 48, 49, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264264154 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264264154 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264264154/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264264154/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264264154 Building ZINC001264264154 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264264154' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264264154 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264264154 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264264154/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264264154 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 938) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/938: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(Cc2ccc(c3ccccc3F)s2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001264264154.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264264154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264264154/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001264264154 none O=C(N1CCN(Cc2ccc(c3ccccc3F)s2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'S.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 14, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 6, 6, 6, 6, 12, 21, 21, 21, 21, 50, 50, 37, 50, 50, 50, 21, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 12, 12, 21, 21, 50, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1] 50 rigid atoms, others: [1, 46, 47, 48, 49, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264264154 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264264154/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264264154 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 939) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/939: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(Cc2ccc(c3ccccc3F)s2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001264264154.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264264154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264264154/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001264264154 none O=C(N1CCN(Cc2ccc(c3ccccc3F)s2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'S.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 14, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 4, 4, 4, 4, 11, 22, 22, 22, 22, 50, 50, 29, 50, 50, 50, 22, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 11, 11, 22, 22, 50, 50, 50, 50, 4, 4, 4, 4, 1, 1, 1, 1] 50 rigid atoms, others: [1, 46, 47, 48, 49, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264264154 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264264154 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264264154/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264264154/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264264154 Building ZINC001264264357 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264264357' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264264357 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264264357 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264264357/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264264357 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 940) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/940 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/940' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccnn2Cc2ccc(C(C)(C)C)cc2)cc1Cl) `ZINC001264264357.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264264357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264264357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001264264357 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccnn2Cc2ccc(C(C)(C)C)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 8, 14, 14, 14, 14, 14, 25, 25, 25, 14, 14, 4, 4, 4, 9, 9, 9, 4, 4, 3, 8, 8, 14, 14, 14, 14, 25, 25, 25, 25, 25, 25, 25, 25, 25, 14, 14, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264264357 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264264357/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264264357 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 941) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/941 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/941' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccnn2Cc2ccc(C(C)(C)C)cc2)cc1Cl) `ZINC001264264357.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264264357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264264357/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001264264357 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccnn2Cc2ccc(C(C)(C)C)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 8, 14, 14, 14, 14, 14, 25, 25, 25, 14, 14, 4, 4, 4, 9, 9, 9, 4, 4, 3, 8, 8, 14, 14, 14, 14, 25, 25, 25, 25, 25, 25, 25, 25, 25, 14, 14, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264264357 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264264357 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264264357/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264264357/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264264357 Building ZINC001264264357 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264264357' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264264357 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264264357 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264264357/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264264357 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 940) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/940: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccnn2Cc2ccc(C(C)(C)C)cc2)cc1Cl) `ZINC001264264357.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264264357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264264357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001264264357 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccnn2Cc2ccc(C(C)(C)C)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 8, 14, 14, 14, 14, 14, 25, 25, 25, 14, 14, 4, 4, 4, 9, 9, 9, 4, 4, 3, 8, 8, 14, 14, 14, 14, 25, 25, 25, 25, 25, 25, 25, 25, 25, 14, 14, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264264357 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264264357/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264264357 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 941) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/941: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccnn2Cc2ccc(C(C)(C)C)cc2)cc1Cl) `ZINC001264264357.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264264357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264264357/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001264264357 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccnn2Cc2ccc(C(C)(C)C)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 8, 14, 14, 14, 14, 14, 25, 25, 25, 14, 14, 4, 4, 4, 9, 9, 9, 4, 4, 3, 8, 8, 14, 14, 14, 14, 25, 25, 25, 25, 25, 25, 25, 25, 25, 14, 14, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264264357 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264264357 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264264357/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264264357/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264264357 Building ZINC001264309025 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264309025' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264309025 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264309025 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264309025/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264309025 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 942) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/942 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/942' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1c(c2ccc(OC)cc2)csc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001264309025.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264309025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264309025/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001264309025 none CCOC(=O)c1c(c2ccc(OC)cc2)csc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 9, 26, 9, 9, 9, 19, 19, 9, 14, 28, 19, 19, 9, 9, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 45, 45, 45, 45, 45, 19, 19, 28, 28, 28, 19, 19, 9, 4, 3, 3, 3, 3] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 245 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264309025 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264309025/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264309025 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 943) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/943 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/943' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1c(c2ccc(OC)cc2)csc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001264309025.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264309025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264309025/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001264309025 none CCOC(=O)c1c(c2ccc(OC)cc2)csc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 9, 26, 9, 9, 9, 19, 19, 9, 9, 29, 19, 19, 9, 9, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 46, 46, 46, 46, 46, 19, 19, 29, 29, 29, 19, 19, 9, 4, 3, 3, 3, 3] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 246 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264309025 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264309025 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264309025/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264309025/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264309025 Building ZINC001264309025 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264309025' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264309025 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264309025 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264309025/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264309025 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 942) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/942: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1c(c2ccc(OC)cc2)csc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001264309025.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264309025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264309025/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001264309025 none CCOC(=O)c1c(c2ccc(OC)cc2)csc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 9, 26, 9, 9, 9, 19, 19, 9, 14, 28, 19, 19, 9, 9, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 45, 45, 45, 45, 45, 19, 19, 28, 28, 28, 19, 19, 9, 4, 3, 3, 3, 3] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 245 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264309025 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264309025/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264309025 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 943) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/943: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1c(c2ccc(OC)cc2)csc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001264309025.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264309025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264309025/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001264309025 none CCOC(=O)c1c(c2ccc(OC)cc2)csc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 9, 26, 9, 9, 9, 19, 19, 9, 9, 29, 19, 19, 9, 9, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 46, 46, 46, 46, 46, 19, 19, 29, 29, 29, 19, 19, 9, 4, 3, 3, 3, 3] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 246 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264309025 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264309025 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264309025/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264309025/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264309025 Building ZINC001264314624 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264314624' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264314624 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264314624 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264314624/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264314624 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 944) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/944 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/944' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCc1ccc(c2cc(NC(=O)[C@@]([O-])([SiH3])c3cnn(CC)c3)n(c3ccccc3)n2)cc1) `ZINC001264314624.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264314624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264314624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001264314624 none CCCc1ccc(c2cc(NC(=O)[C@@]([O-])([SiH3])c3cnn(CC)c3)n(c3ccccc3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 26, 25, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 9, 5, 4, 4, 4, 4, 4, 4, 4, 4, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 4, 2, 5, 9, 9, 9, 9, 9, 5, 4, 4, 4, 4, 4, 26, 26] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264314624 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264314624/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264314624 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 945) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/945 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/945' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCc1ccc(c2cc(NC(=O)[C@]([O-])([SiH3])c3cnn(CC)c3)n(c3ccccc3)n2)cc1) `ZINC001264314624.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264314624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264314624/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001264314624 none CCCc1ccc(c2cc(NC(=O)[C@]([O-])([SiH3])c3cnn(CC)c3)n(c3ccccc3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 26, 26, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 9, 5, 4, 4, 4, 4, 4, 4, 4, 4, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 4, 2, 5, 9, 9, 9, 9, 9, 5, 4, 4, 4, 4, 4, 26, 26] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264314624 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264314624 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264314624/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264314624/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264314624 Building ZINC001264314624 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264314624' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264314624 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264314624 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264314624/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264314624 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 944) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/944: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCc1ccc(c2cc(NC(=O)[C@@]([O-])([SiH3])c3cnn(CC)c3)n(c3ccccc3)n2)cc1) `ZINC001264314624.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264314624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264314624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001264314624 none CCCc1ccc(c2cc(NC(=O)[C@@]([O-])([SiH3])c3cnn(CC)c3)n(c3ccccc3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 26, 25, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 9, 5, 4, 4, 4, 4, 4, 4, 4, 4, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 4, 2, 5, 9, 9, 9, 9, 9, 5, 4, 4, 4, 4, 4, 26, 26] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264314624 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264314624/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264314624 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 945) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/945: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCc1ccc(c2cc(NC(=O)[C@]([O-])([SiH3])c3cnn(CC)c3)n(c3ccccc3)n2)cc1) `ZINC001264314624.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264314624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264314624/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001264314624 none CCCc1ccc(c2cc(NC(=O)[C@]([O-])([SiH3])c3cnn(CC)c3)n(c3ccccc3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 26, 26, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 9, 5, 4, 4, 4, 4, 4, 4, 4, 4, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 4, 2, 5, 9, 9, 9, 9, 9, 5, 4, 4, 4, 4, 4, 26, 26] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264314624 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264314624 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264314624/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264314624/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264314624 Building ZINC001264327784 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264327784' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264327784 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264327784 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264327784/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264327784 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 946) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/946 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/946' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1OCc1ccncc1) `ZINC001264327784.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264327784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264327784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001264327784 none COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1OCc1ccncc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 6, 6, 6, 29, 39, 50, 50, 49, 50, 50, 12, 12, 12, 6, 6, 2, 2, 1, 2, 6, 39, 39, 50, 50, 50, 50] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264327784 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264327784/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264327784 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 947) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/947 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/947' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1OCc1ccncc1) `ZINC001264327784.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264327784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264327784/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001264327784 none COc1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1OCc1ccncc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 6, 6, 6, 30, 40, 50, 50, 49, 50, 50, 12, 12, 12, 6, 6, 2, 2, 1, 2, 6, 40, 40, 50, 50, 50, 50] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264327784 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264327784 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264327784/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264327784/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264327784 Building ZINC001264327784 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264327784' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264327784 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264327784 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264327784/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264327784 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 946) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/946: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1OCc1ccncc1) `ZINC001264327784.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264327784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264327784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001264327784 none COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1OCc1ccncc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 6, 6, 6, 29, 39, 50, 50, 49, 50, 50, 12, 12, 12, 6, 6, 2, 2, 1, 2, 6, 39, 39, 50, 50, 50, 50] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264327784 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264327784/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264327784 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 947) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/947: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1OCc1ccncc1) `ZINC001264327784.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264327784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264327784/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001264327784 none COc1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1OCc1ccncc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 6, 6, 6, 30, 40, 50, 50, 49, 50, 50, 12, 12, 12, 6, 6, 2, 2, 1, 2, 6, 40, 40, 50, 50, 50, 50] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264327784 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264327784 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264327784/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264327784/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264327784 Building ZINC001264329792 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264329792' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264329792 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264329792 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264329792/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264329792 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 948) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/948 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/948' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1)c1cccs1) `ZINC001264329792.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264329792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264329792/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001264329792 none O=C(Nc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1)c1cccs1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 14, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 25, 13, 13, 13, 13, 13, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 13, 25, 33, 33, 33, 33, 26, 13, 13, 13, 3, 7, 7, 13, 33, 33, 33] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264329792 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264329792/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264329792 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 949) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/949 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/949' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1)c1cccs1) `ZINC001264329792.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264329792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264329792/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001264329792 none O=C(Nc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1)c1cccs1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 14, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 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] 0 hydrogens 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, 13, 13, 13, 13, 13, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 13, 27, 34, 34, 34, 34, 27, 13, 13, 13, 3, 7, 7, 13, 34, 34, 34] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264329792 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264329792 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264329792/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264329792/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264329792 Building ZINC001264329792 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264329792' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264329792 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264329792 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264329792/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264329792 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 948) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/948: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1)c1cccs1) `ZINC001264329792.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264329792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264329792/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001264329792 none O=C(Nc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1)c1cccs1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 14, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 25, 13, 13, 13, 13, 13, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 13, 25, 33, 33, 33, 33, 26, 13, 13, 13, 3, 7, 7, 13, 33, 33, 33] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264329792 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264329792/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264329792 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 949) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/949: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1)c1cccs1) `ZINC001264329792.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264329792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264329792/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001264329792 none O=C(Nc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1)c1cccs1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 14, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 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] 0 hydrogens 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, 13, 13, 13, 13, 13, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 13, 27, 34, 34, 34, 34, 27, 13, 13, 13, 3, 7, 7, 13, 34, 34, 34] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264329792 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264329792 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264329792/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264329792/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264329792 Building ZINC001264395922 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264395922' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264395922 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264395922 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264395922/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264395922 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 950) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/950 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/950' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(c2ccc([C@H](C)NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)cs1) `ZINC001264395922.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264395922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264395922/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001264395922 none Cc1nc(c2ccc([C@H](C)NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 14, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 7, 3, 16, 16, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 16, 16, 30, 30, 30, 30, 30, 16, 16, 3, 3, 3, 2, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 16, 16, 30] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 90 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264395922 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264395922/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264395922 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 951) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/951 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/951' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(c2ccc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)cs1) `ZINC001264395922.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264395922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264395922/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001264395922 none Cc1nc(c2ccc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 14, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 6, 5, 16, 16, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 16, 16, 31, 31, 31, 31, 31, 16, 16, 3, 3, 3, 2, 3, 3, 3, 6, 6, 4, 6, 6, 3, 3, 3, 16, 16, 30] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 98 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264395922 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264395922 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264395922/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264395922/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264395922 Building ZINC001264395922 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264395922' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264395922 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264395922 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264395922/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264395922 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 950) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/950: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(c2ccc([C@H](C)NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)cs1) `ZINC001264395922.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264395922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264395922/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001264395922 none Cc1nc(c2ccc([C@H](C)NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 14, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 7, 3, 16, 16, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 16, 16, 30, 30, 30, 30, 30, 16, 16, 3, 3, 3, 2, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 16, 16, 30] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 90 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264395922 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264395922/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264395922 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 951) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/951: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(c2ccc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)cs1) `ZINC001264395922.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264395922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264395922/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001264395922 none Cc1nc(c2ccc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 14, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 6, 5, 16, 16, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 16, 16, 31, 31, 31, 31, 31, 16, 16, 3, 3, 3, 2, 3, 3, 3, 6, 6, 4, 6, 6, 3, 3, 3, 16, 16, 30] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 98 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264395922 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264395922 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264395922/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264395922/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264395922 Building ZINC001264395923 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264395923' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264395923 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264395923 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264395923/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264395923 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 952) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/952 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/952' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(c2ccc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)cs1) `ZINC001264395923.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264395923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264395923/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001264395923 none Cc1nc(c2ccc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 14, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 6, 5, 16, 16, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 16, 16, 31, 31, 31, 31, 31, 16, 16, 3, 3, 3, 2, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 16, 16, 31] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 84 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264395923 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264395923/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264395923 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 953) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/953 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/953' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(c2ccc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)cs1) `ZINC001264395923.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264395923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264395923/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001264395923 none Cc1nc(c2ccc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 14, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 4, 4, 15, 15, 4, 2, 4, 4, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 15, 15, 28, 28, 28, 28, 28, 15, 15, 4, 4, 4, 2, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 15, 15, 28] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 97 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264395923 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264395923 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264395923/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264395923/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264395923 Building ZINC001264395923 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264395923' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264395923 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264395923 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264395923/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264395923 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 952) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/952: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(c2ccc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)cs1) `ZINC001264395923.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264395923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264395923/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001264395923 none Cc1nc(c2ccc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 14, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 6, 5, 16, 16, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 16, 16, 31, 31, 31, 31, 31, 16, 16, 3, 3, 3, 2, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 16, 16, 31] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 84 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264395923 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264395923/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264395923 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 953) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/953: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(c2ccc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)cs1) `ZINC001264395923.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264395923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264395923/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001264395923 none Cc1nc(c2ccc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 14, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 4, 4, 15, 15, 4, 2, 4, 4, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 15, 15, 28, 28, 28, 28, 28, 15, 15, 4, 4, 4, 2, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 15, 15, 28] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 97 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264395923 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264395923 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264395923/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264395923/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264395923 Building ZINC001264409535 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264409535' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264409535 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264409535 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264409535/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264409535 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 954) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/954 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/954' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)c1ccc(Cl)cc1)CCC2) `ZINC001264409535.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264409535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264409535/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001264409535 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)c1ccc(Cl)cc1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 6, 6, 6, 24, 24, 24, 24, 24, 42, 42, 43, 43, 42, 42, 43, 43, 24, 24, 24, 5, 5, 5, 5, 5, 5, 5, 6, 43, 43, 43, 43, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264409535 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264409535/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264409535 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 955) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/955 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/955' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)c1ccc(Cl)cc1)CCC2) `ZINC001264409535.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264409535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264409535/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001264409535 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)c1ccc(Cl)cc1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 6, 6, 6, 20, 20, 20, 20, 20, 38, 38, 40, 40, 38, 39, 40, 40, 20, 20, 20, 6, 6, 6, 5, 5, 5, 5, 6, 40, 40, 40, 40, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264409535 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264409535 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264409535/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264409535/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264409535 Building ZINC001264409535 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264409535' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264409535 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264409535 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264409535/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264409535 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 954) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/954: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)c1ccc(Cl)cc1)CCC2) `ZINC001264409535.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264409535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264409535/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001264409535 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)c1ccc(Cl)cc1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 6, 6, 6, 24, 24, 24, 24, 24, 42, 42, 43, 43, 42, 42, 43, 43, 24, 24, 24, 5, 5, 5, 5, 5, 5, 5, 6, 43, 43, 43, 43, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264409535 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264409535/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264409535 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 955) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/955: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)c1ccc(Cl)cc1)CCC2) `ZINC001264409535.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264409535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264409535/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001264409535 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)c1ccc(Cl)cc1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 6, 6, 6, 20, 20, 20, 20, 20, 38, 38, 40, 40, 38, 39, 40, 40, 20, 20, 20, 6, 6, 6, 5, 5, 5, 5, 6, 40, 40, 40, 40, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264409535 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264409535 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264409535/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264409535/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264409535 Building ZINC001264425163 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264425163' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264425163 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264425163 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264425163/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264425163 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 956) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/956 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/956' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(Cc1ccc(Br)cc1)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001264425163.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264425163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264425163/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001264425163 none CC(C)N(Cc1ccc(Br)cc1)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 1, 1, 1, 17, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 16, 4, 10, 28, 34, 34, 30, 34, 34, 34, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 16, 16, 16, 16, 16, 16, 16, 28, 28, 34, 34, 34, 34, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 164 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264425163 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264425163/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264425163 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 957) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/957 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/957' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(Cc1ccc(Br)cc1)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001264425163.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264425163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264425163/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001264425163 none CC(C)N(Cc1ccc(Br)cc1)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 1, 1, 1, 17, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 16, 4, 10, 28, 34, 34, 33, 34, 34, 34, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 16, 16, 16, 16, 16, 16, 16, 28, 28, 34, 34, 34, 34, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 149 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264425163 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264425163 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264425163/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264425163/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264425163 Building ZINC001264425163 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264425163' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264425163 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264425163 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264425163/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264425163 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 956) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/956: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(Cc1ccc(Br)cc1)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001264425163.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264425163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264425163/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001264425163 none CC(C)N(Cc1ccc(Br)cc1)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 1, 1, 1, 17, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 16, 4, 10, 28, 34, 34, 30, 34, 34, 34, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 16, 16, 16, 16, 16, 16, 16, 28, 28, 34, 34, 34, 34, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 164 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264425163 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264425163/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264425163 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 957) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/957: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(Cc1ccc(Br)cc1)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001264425163.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264425163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264425163/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001264425163 none CC(C)N(Cc1ccc(Br)cc1)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 1, 1, 1, 17, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 16, 4, 10, 28, 34, 34, 33, 34, 34, 34, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 16, 16, 16, 16, 16, 16, 16, 28, 28, 34, 34, 34, 34, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 149 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264425163 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264425163 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264425163/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264425163/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264425163 Building ZINC001264475501 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264475501' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264475501 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264475501 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264475501/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264475501 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 958) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/958 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/958' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Cl)c(Cl)c1)[C@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001264475501.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264475501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264475501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001264475501 none O=C(Nc1ccc(Cl)c(Cl)c1)[C@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 16, 1, 16, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 10, 10, 32, 32, 32, 32, 32, 32, 32, 6, 6, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 10, 32, 32, 32, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264475501 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264475501/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264475501 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 959) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/959 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/959' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Cl)c(Cl)c1)[C@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001264475501.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264475501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264475501/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001264475501 none O=C(Nc1ccc(Cl)c(Cl)c1)[C@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 16, 1, 16, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 10, 10, 31, 31, 30, 31, 31, 31, 31, 5, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 10, 31, 31, 31, 5, 5, 5, 5, 5, 5, 5, 5, 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264475501 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264475501 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264475501/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264475501/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264475501 Building ZINC001264475501 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264475501' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264475501 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264475501 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264475501/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264475501 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 958) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/958: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Cl)c(Cl)c1)[C@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001264475501.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264475501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264475501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001264475501 none O=C(Nc1ccc(Cl)c(Cl)c1)[C@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 16, 1, 16, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 10, 10, 32, 32, 32, 32, 32, 32, 32, 6, 6, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 10, 32, 32, 32, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264475501 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264475501/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264475501 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 959) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/959: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Cl)c(Cl)c1)[C@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001264475501.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264475501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264475501/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001264475501 none O=C(Nc1ccc(Cl)c(Cl)c1)[C@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 16, 1, 16, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 10, 10, 31, 31, 30, 31, 31, 31, 31, 5, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 10, 31, 31, 31, 5, 5, 5, 5, 5, 5, 5, 5, 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264475501 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264475501 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264475501/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264475501/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264475501 Building ZINC001264475502 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264475502' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264475502 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264475502 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264475502/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264475502 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 960) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/960 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/960' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Cl)c(Cl)c1)[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001264475502.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264475502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264475502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001264475502 none O=C(Nc1ccc(Cl)c(Cl)c1)[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 16, 1, 16, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 10, 10, 31, 31, 29, 31, 31, 31, 31, 5, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 10, 31, 31, 31, 5, 5, 5, 5, 5, 5, 5, 5, 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]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264475502 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264475502/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264475502 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 961) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/961 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/961' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Cl)c(Cl)c1)[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001264475502.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264475502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264475502/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001264475502 none O=C(Nc1ccc(Cl)c(Cl)c1)[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 16, 1, 16, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 10, 10, 32, 32, 32, 32, 32, 32, 32, 6, 6, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 10, 32, 32, 32, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264475502 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264475502 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264475502/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264475502/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264475502 Building ZINC001264475502 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264475502' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264475502 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264475502 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264475502/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264475502 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 960) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/960: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Cl)c(Cl)c1)[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001264475502.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264475502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264475502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001264475502 none O=C(Nc1ccc(Cl)c(Cl)c1)[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 16, 1, 16, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 10, 10, 31, 31, 29, 31, 31, 31, 31, 5, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 10, 31, 31, 31, 5, 5, 5, 5, 5, 5, 5, 5, 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]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264475502 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264475502/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264475502 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 961) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/961: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Cl)c(Cl)c1)[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001264475502.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264475502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264475502/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001264475502 none O=C(Nc1ccc(Cl)c(Cl)c1)[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 16, 1, 16, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 10, 10, 32, 32, 32, 32, 32, 32, 32, 6, 6, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 10, 32, 32, 32, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264475502 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264475502 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264475502/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264475502/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264475502 Building ZINC001264479179 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264479179' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264479179 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264479179 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264479179/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264479179 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 962) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/962 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/962' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(Cl)cc(Cl)c1)[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001264479179.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264479179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264479179/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001264479179 none O=C(Nc1cc(Cl)cc(Cl)c1)[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 11, 23, 23, 34, 34, 34, 23, 34, 34, 34, 11, 11, 11, 11, 11, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 9, 23, 34, 26, 34, 11, 11, 11, 11, 11, 11, 9, 9] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264479179 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264479179/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264479179 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 963) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/963 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/963' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(Cl)cc(Cl)c1)[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001264479179.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264479179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264479179/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001264479179 none O=C(Nc1cc(Cl)cc(Cl)c1)[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 9, 21, 21, 33, 33, 33, 33, 33, 33, 33, 9, 9, 9, 9, 9, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 21, 33, 33, 33, 9, 9, 9, 9, 9, 9, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264479179 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264479179 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264479179/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264479179/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264479179 Building ZINC001264479179 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264479179' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264479179 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264479179 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264479179/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264479179 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 962) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/962: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(Cl)cc(Cl)c1)[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001264479179.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264479179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264479179/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001264479179 none O=C(Nc1cc(Cl)cc(Cl)c1)[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 11, 23, 23, 34, 34, 34, 23, 34, 34, 34, 11, 11, 11, 11, 11, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 9, 23, 34, 26, 34, 11, 11, 11, 11, 11, 11, 9, 9] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264479179 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264479179/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264479179 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 963) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/963: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(Cl)cc(Cl)c1)[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001264479179.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264479179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264479179/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001264479179 none O=C(Nc1cc(Cl)cc(Cl)c1)[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 9, 21, 21, 33, 33, 33, 33, 33, 33, 33, 9, 9, 9, 9, 9, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 21, 33, 33, 33, 9, 9, 9, 9, 9, 9, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264479179 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264479179 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264479179/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264479179/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264479179 Building ZINC001264479180 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264479180' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264479180 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264479180 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264479180/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264479180 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 964) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/964 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/964' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(Cl)cc(Cl)c1)[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001264479180.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264479180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264479180/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001264479180 none O=C(Nc1cc(Cl)cc(Cl)c1)[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 8, 20, 20, 35, 35, 35, 20, 35, 35, 35, 8, 8, 8, 8, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 20, 35, 23, 35, 8, 8, 8, 8, 8, 8, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264479180 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264479180/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264479180 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 965) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/965 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/965' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(Cl)cc(Cl)c1)[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001264479180.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264479180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264479180/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001264479180 none O=C(Nc1cc(Cl)cc(Cl)c1)[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 12, 23, 23, 34, 34, 34, 23, 34, 34, 34, 12, 12, 12, 12, 12, 7, 1, 7, 1, 1, 1, 9, 9, 9, 9, 9, 23, 34, 25, 34, 12, 12, 12, 12, 12, 12, 9, 9] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264479180 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264479180 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264479180/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264479180/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264479180 Building ZINC001264479180 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264479180' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264479180 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264479180 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264479180/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264479180 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 964) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/964: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(Cl)cc(Cl)c1)[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001264479180.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264479180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264479180/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001264479180 none O=C(Nc1cc(Cl)cc(Cl)c1)[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 8, 20, 20, 35, 35, 35, 20, 35, 35, 35, 8, 8, 8, 8, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 20, 35, 23, 35, 8, 8, 8, 8, 8, 8, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264479180 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264479180/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264479180 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 965) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/965: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(Cl)cc(Cl)c1)[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001264479180.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264479180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264479180/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001264479180 none O=C(Nc1cc(Cl)cc(Cl)c1)[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 12, 23, 23, 34, 34, 34, 23, 34, 34, 34, 12, 12, 12, 12, 12, 7, 1, 7, 1, 1, 1, 9, 9, 9, 9, 9, 23, 34, 25, 34, 12, 12, 12, 12, 12, 12, 9, 9] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264479180 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264479180 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264479180/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264479180/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264479180 Building ZINC001264483379 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264483379' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264483379 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264483379 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264483379/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264483379 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 966) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/966 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/966' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(C(C)(C)C)nn2c2ccc(F)cc2)cc1Cl) `ZINC001264483379.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264483379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264483379/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001264483379 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(C(C)(C)C)nn2c2ccc(F)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 16, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 6, 6, 1, 1, 1, 1, 4, 4, 5, 9, 9, 9, 15, 15, 15, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 6, 6, 12, 12, 12, 6, 6, 5, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 9, 9, 9, 9, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 86 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264483379 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264483379/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264483379 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 967) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/967 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/967' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(C(C)(C)C)nn2c2ccc(F)cc2)cc1Cl) `ZINC001264483379.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264483379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264483379/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001264483379 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(C(C)(C)C)nn2c2ccc(F)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 16, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 3, 3, 4, 8, 8, 8, 14, 14, 14, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 6, 6, 12, 12, 12, 6, 6, 4, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 8, 8, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 86 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264483379 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264483379 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264483379/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264483379/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264483379 Building ZINC001264483379 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264483379' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264483379 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264483379 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264483379/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264483379 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 966) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/966: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(C(C)(C)C)nn2c2ccc(F)cc2)cc1Cl) `ZINC001264483379.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264483379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264483379/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001264483379 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(C(C)(C)C)nn2c2ccc(F)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 16, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 6, 6, 1, 1, 1, 1, 4, 4, 5, 9, 9, 9, 15, 15, 15, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 6, 6, 12, 12, 12, 6, 6, 5, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 9, 9, 9, 9, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 86 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264483379 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264483379/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264483379 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 967) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/967: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(C(C)(C)C)nn2c2ccc(F)cc2)cc1Cl) `ZINC001264483379.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264483379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264483379/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001264483379 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(C(C)(C)C)nn2c2ccc(F)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 16, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 3, 3, 4, 8, 8, 8, 14, 14, 14, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 6, 6, 12, 12, 12, 6, 6, 4, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 8, 8, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 86 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264483379 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264483379 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264483379/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264483379/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264483379 Building ZINC001264533116 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264533116' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264533116 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264533116 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264533116/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264533116 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 968) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/968 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/968' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)c2ccccc2)cc1C(F)(F)F) `ZINC001264533116.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264533116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264533116/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001264533116 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)c2ccccc2)cc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 6, 6, 6, 13, 13, 6, 6, 27, 28, 27, 38, 38, 29, 38, 38, 13, 13, 13, 13, 13, 13, 5, 5, 5, 5, 5, 5, 5, 6, 13, 13, 28, 38, 38, 34, 38, 38, 13] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264533116 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264533116/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264533116 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 969) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/969 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/969' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)c2ccccc2)cc1C(F)(F)F) `ZINC001264533116.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264533116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264533116/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001264533116 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)c2ccccc2)cc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 6, 6, 6, 14, 14, 6, 12, 31, 35, 34, 44, 44, 44, 44, 44, 14, 14, 14, 14, 14, 14, 4, 4, 4, 4, 4, 4, 4, 6, 14, 14, 35, 44, 44, 44, 44, 44, 14] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264533116 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264533116 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264533116/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264533116/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264533116 Building ZINC001264533116 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264533116' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264533116 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264533116 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264533116/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264533116 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 968) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/968: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)c2ccccc2)cc1C(F)(F)F) `ZINC001264533116.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264533116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264533116/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001264533116 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)c2ccccc2)cc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 6, 6, 6, 13, 13, 6, 6, 27, 28, 27, 38, 38, 29, 38, 38, 13, 13, 13, 13, 13, 13, 5, 5, 5, 5, 5, 5, 5, 6, 13, 13, 28, 38, 38, 34, 38, 38, 13] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264533116 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264533116/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264533116 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 969) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/969: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)c2ccccc2)cc1C(F)(F)F) `ZINC001264533116.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264533116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264533116/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001264533116 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)c2ccccc2)cc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 6, 6, 6, 14, 14, 6, 12, 31, 35, 34, 44, 44, 44, 44, 44, 14, 14, 14, 14, 14, 14, 4, 4, 4, 4, 4, 4, 4, 6, 14, 14, 35, 44, 44, 44, 44, 44, 14] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264533116 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264533116 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264533116/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264533116/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264533116 Building ZINC001264535554 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264535554' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264535554 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264535554 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264535554/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264535554 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 970) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/970 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/970' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(N(C)C)cc1C) `ZINC001264535554.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264535554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264535554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001264535554 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(N(C)C)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 21, 21, 3, 21, 21, 21, 21, 21, 21, 3, 3, 1, 1, 1, 1, 4, 4, 4, 7, 7, 6, 7, 10, 10, 7, 7, 7, 3, 3, 3, 21, 21, 3, 21, 3, 3, 3, 4, 7, 7, 10, 10, 10, 10, 10, 10, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 79 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264535554 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264535554/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264535554 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 971) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/971 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/971' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(N(C)C)cc1C) `ZINC001264535554.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264535554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264535554/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001264535554 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(N(C)C)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 19, 19, 3, 19, 19, 19, 19, 19, 19, 3, 3, 1, 1, 1, 1, 4, 4, 4, 7, 7, 4, 6, 11, 11, 7, 7, 7, 3, 3, 3, 19, 19, 3, 19, 3, 3, 3, 4, 7, 7, 11, 11, 11, 11, 11, 11, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 85 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264535554 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264535554 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264535554/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264535554/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264535554 Building ZINC001264535554 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264535554' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264535554 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264535554 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264535554/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264535554 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 970) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/970: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(N(C)C)cc1C) `ZINC001264535554.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264535554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264535554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001264535554 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(N(C)C)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 21, 21, 3, 21, 21, 21, 21, 21, 21, 3, 3, 1, 1, 1, 1, 4, 4, 4, 7, 7, 6, 7, 10, 10, 7, 7, 7, 3, 3, 3, 21, 21, 3, 21, 3, 3, 3, 4, 7, 7, 10, 10, 10, 10, 10, 10, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 79 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264535554 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264535554/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264535554 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 971) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/971: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(N(C)C)cc1C) `ZINC001264535554.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264535554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264535554/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001264535554 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(N(C)C)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 19, 19, 3, 19, 19, 19, 19, 19, 19, 3, 3, 1, 1, 1, 1, 4, 4, 4, 7, 7, 4, 6, 11, 11, 7, 7, 7, 3, 3, 3, 19, 19, 3, 19, 3, 3, 3, 4, 7, 7, 11, 11, 11, 11, 11, 11, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 85 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264535554 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264535554 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264535554/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264535554/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264535554 Building ZINC001264538429 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264538429' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264538429 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264538429 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264538429/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264538429 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 972) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/972 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/972' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2Oc2ncc(Cl)cc2Cl)cn1) `ZINC001264538429.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264538429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264538429/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001264538429 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2Oc2ncc(Cl)cc2Cl)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 1, 8, 1, 1, 16, 1, 1, 16, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 13, 13, 6, 6, 1, 1, 1, 1, 4, 4, 4, 8, 8, 6, 8, 8, 8, 19, 24, 24, 24, 24, 24, 24, 24, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 4, 8, 8, 8, 8, 24, 24, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264538429 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264538429/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264538429 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 973) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/973 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/973' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccccc2Oc2ncc(Cl)cc2Cl)cn1) `ZINC001264538429.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264538429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264538429/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001264538429 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccccc2Oc2ncc(Cl)cc2Cl)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 1, 8, 1, 1, 16, 1, 1, 16, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 1, 1, 1, 1, 4, 4, 4, 7, 7, 6, 7, 7, 7, 20, 25, 25, 25, 25, 25, 25, 25, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 4, 7, 7, 7, 7, 25, 25, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264538429 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264538429 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264538429/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264538429/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264538429 Building ZINC001264538429 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264538429' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264538429 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264538429 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264538429/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264538429 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 972) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/972: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2Oc2ncc(Cl)cc2Cl)cn1) `ZINC001264538429.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264538429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264538429/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001264538429 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2Oc2ncc(Cl)cc2Cl)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 1, 8, 1, 1, 16, 1, 1, 16, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 13, 13, 6, 6, 1, 1, 1, 1, 4, 4, 4, 8, 8, 6, 8, 8, 8, 19, 24, 24, 24, 24, 24, 24, 24, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 4, 8, 8, 8, 8, 24, 24, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264538429 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264538429/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264538429 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 973) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/973: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccccc2Oc2ncc(Cl)cc2Cl)cn1) `ZINC001264538429.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264538429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264538429/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001264538429 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccccc2Oc2ncc(Cl)cc2Cl)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 1, 8, 1, 1, 16, 1, 1, 16, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 1, 1, 1, 1, 4, 4, 4, 7, 7, 6, 7, 7, 7, 20, 25, 25, 25, 25, 25, 25, 25, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 4, 7, 7, 7, 7, 25, 25, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264538429 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264538429 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264538429/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264538429/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264538429 Building ZINC001264554858 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264554858' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264554858 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264554858 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264554858/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264554858 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 974) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/974 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/974' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(COCc2ccccc2)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001264554858.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264554858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264554858/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001264554858 none O=C(NCc1ccc(COCc2ccccc2)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 6, 10, 10, 8, 10, 24, 24, 50, 50, 50, 50, 50, 50, 10, 10, 1, 1, 1, 2, 2, 2, 2, 2, 2, 6, 6, 10, 10, 24, 24, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264554858 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264554858/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264554858 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 975) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/975 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/975' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(COCc2ccccc2)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001264554858.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264554858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264554858/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001264554858 none O=C(NCc1ccc(COCc2ccccc2)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 6, 10, 10, 6, 6, 24, 24, 50, 50, 50, 50, 50, 50, 10, 10, 1, 1, 1, 2, 2, 2, 2, 2, 2, 6, 6, 10, 10, 24, 24, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264554858 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264554858 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264554858/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264554858/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264554858 Building ZINC001264554858 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264554858' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264554858 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264554858 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264554858/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264554858 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 974) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/974: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(COCc2ccccc2)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001264554858.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264554858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264554858/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001264554858 none O=C(NCc1ccc(COCc2ccccc2)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 6, 10, 10, 8, 10, 24, 24, 50, 50, 50, 50, 50, 50, 10, 10, 1, 1, 1, 2, 2, 2, 2, 2, 2, 6, 6, 10, 10, 24, 24, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264554858 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264554858/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264554858 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 975) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/975: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(COCc2ccccc2)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001264554858.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264554858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264554858/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001264554858 none O=C(NCc1ccc(COCc2ccccc2)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 6, 10, 10, 6, 6, 24, 24, 50, 50, 50, 50, 50, 50, 10, 10, 1, 1, 1, 2, 2, 2, 2, 2, 2, 6, 6, 10, 10, 24, 24, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264554858 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264554858 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264554858/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264554858/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264554858 Building ZINC001264578606 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264578606' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264578606 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264578606 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264578606/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264578606 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 976) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/976 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/976' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(c2ncc3n2CCCC3)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001264578606.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264578606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264578606/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001264578606 none O=C(Nc1ccc(c2ncc3n2CCCC3)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 8, 8, 8, 8, 28, 28, 28, 28, 28, 28, 28, 28, 8, 8, 1, 1, 1, 10, 10, 10, 10, 10, 4, 8, 8, 28, 28, 28, 28, 28, 28, 28, 28, 28, 8, 8, 10, 10] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264578606 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264578606/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264578606 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 977) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/977 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/977' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(c2ncc3n2CCCC3)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001264578606.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264578606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264578606/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001264578606 none O=C(Nc1ccc(c2ncc3n2CCCC3)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 3, 8, 29, 29, 29, 29, 29, 29, 29, 29, 8, 8, 1, 1, 1, 10, 10, 10, 10, 10, 3, 8, 8, 29, 29, 29, 29, 29, 29, 29, 29, 29, 8, 8, 10, 10] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264578606 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264578606 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264578606/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264578606/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264578606 Building ZINC001264578606 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264578606' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264578606 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264578606 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264578606/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264578606 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 976) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/976: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(c2ncc3n2CCCC3)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001264578606.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264578606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264578606/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001264578606 none O=C(Nc1ccc(c2ncc3n2CCCC3)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 8, 8, 8, 8, 28, 28, 28, 28, 28, 28, 28, 28, 8, 8, 1, 1, 1, 10, 10, 10, 10, 10, 4, 8, 8, 28, 28, 28, 28, 28, 28, 28, 28, 28, 8, 8, 10, 10] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264578606 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264578606/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264578606 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 977) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/977: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(c2ncc3n2CCCC3)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001264578606.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264578606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264578606/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001264578606 none O=C(Nc1ccc(c2ncc3n2CCCC3)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 3, 8, 29, 29, 29, 29, 29, 29, 29, 29, 8, 8, 1, 1, 1, 10, 10, 10, 10, 10, 3, 8, 8, 29, 29, 29, 29, 29, 29, 29, 29, 29, 8, 8, 10, 10] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264578606 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264578606 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264578606/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264578606/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264578606 Building ZINC001264581674 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264581674' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264581674 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264581674 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264581674/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264581674 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 978) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/978 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/978' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2cc(NC(=O)[C@@]([O-])([SiH3])c3ccccc3OC)n(c3cccc(C)c3)n2)cc1) `ZINC001264581674.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264581674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264581674/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001264581674 none COc1ccc(c2cc(NC(=O)[C@@]([O-])([SiH3])c3ccccc3OC)n(c3cccc(C)c3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 8, 1, 1, 1, 1, 1, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 8, 8, 8, 6, 4, 1, 4, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 8, 8, 15, 15, 15, 15, 15, 15, 8, 28, 28, 28, 28, 28, 28, 28, 8, 6, 2, 2, 2, 2, 2, 2, 2, 15, 15, 15, 15, 15, 15, 15, 28, 28] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264581674 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264581674/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264581674 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 979) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/979 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/979' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2cc(NC(=O)[C@]([O-])([SiH3])c3ccccc3OC)n(c3cccc(C)c3)n2)cc1) `ZINC001264581674.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264581674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264581674/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001264581674 none COc1ccc(c2cc(NC(=O)[C@]([O-])([SiH3])c3ccccc3OC)n(c3cccc(C)c3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 8, 1, 1, 1, 1, 1, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 30, 30, 10, 10, 10, 6, 4, 1, 4, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 10, 10, 17, 17, 17, 17, 17, 17, 10, 30, 30, 30, 30, 30, 30, 30, 10, 6, 2, 2, 2, 2, 2, 2, 2, 17, 17, 17, 17, 17, 17, 17, 30, 30] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264581674 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264581674 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264581674/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264581674/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264581674 Building ZINC001264581674 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264581674' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264581674 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264581674 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264581674/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264581674 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 978) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/978: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2cc(NC(=O)[C@@]([O-])([SiH3])c3ccccc3OC)n(c3cccc(C)c3)n2)cc1) `ZINC001264581674.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264581674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264581674/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001264581674 none COc1ccc(c2cc(NC(=O)[C@@]([O-])([SiH3])c3ccccc3OC)n(c3cccc(C)c3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 8, 1, 1, 1, 1, 1, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 8, 8, 8, 6, 4, 1, 4, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 8, 8, 15, 15, 15, 15, 15, 15, 8, 28, 28, 28, 28, 28, 28, 28, 8, 6, 2, 2, 2, 2, 2, 2, 2, 15, 15, 15, 15, 15, 15, 15, 28, 28] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264581674 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264581674/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264581674 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 979) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/979: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2cc(NC(=O)[C@]([O-])([SiH3])c3ccccc3OC)n(c3cccc(C)c3)n2)cc1) `ZINC001264581674.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264581674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264581674/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001264581674 none COc1ccc(c2cc(NC(=O)[C@]([O-])([SiH3])c3ccccc3OC)n(c3cccc(C)c3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 8, 1, 1, 1, 1, 1, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 30, 30, 10, 10, 10, 6, 4, 1, 4, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 10, 10, 17, 17, 17, 17, 17, 17, 10, 30, 30, 30, 30, 30, 30, 30, 10, 6, 2, 2, 2, 2, 2, 2, 2, 17, 17, 17, 17, 17, 17, 17, 30, 30] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264581674 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264581674 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264581674/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264581674/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264581674 Building ZINC001264587634 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264587634' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264587634 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264587634 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264587634/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264587634 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 980) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/980 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/980' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(OCCCC(=O)Nc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3cccc(C)c3)cc2)cc1) `ZINC001264587634.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264587634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264587634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001264587634 none Cc1ccc(OCCCC(=O)Nc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3cccc(C)c3)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 29, 29, 29, 29, 17, 17, 17, 13, 8, 13, 13, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 13, 13, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 17, 13, 13, 6, 6, 1, 2, 2, 2, 2, 2, 2, 2, 13, 13, 29, 29] 50 rigid atoms, others: [49, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264587634 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264587634/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264587634 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 981) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/981 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/981' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(OCCCC(=O)Nc2ccc(CNC(=O)[C@]([O-])([SiH3])c3cccc(C)c3)cc2)cc1) `ZINC001264587634.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264587634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264587634/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001264587634 none Cc1ccc(OCCCC(=O)Nc2ccc(CNC(=O)[C@]([O-])([SiH3])c3cccc(C)c3)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 29, 29, 29, 29, 17, 17, 17, 13, 10, 13, 13, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 13, 13, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 17, 13, 13, 6, 6, 1, 2, 2, 2, 2, 2, 2, 2, 13, 13, 29, 29] 50 rigid atoms, others: [49, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264587634 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264587634 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264587634/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264587634/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264587634 Building ZINC001264587634 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264587634' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264587634 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264587634 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264587634/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264587634 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 980) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/980: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(OCCCC(=O)Nc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3cccc(C)c3)cc2)cc1) `ZINC001264587634.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264587634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264587634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001264587634 none Cc1ccc(OCCCC(=O)Nc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3cccc(C)c3)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 29, 29, 29, 29, 17, 17, 17, 13, 8, 13, 13, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 13, 13, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 17, 13, 13, 6, 6, 1, 2, 2, 2, 2, 2, 2, 2, 13, 13, 29, 29] 50 rigid atoms, others: [49, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264587634 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264587634/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264587634 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 981) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/981: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(OCCCC(=O)Nc2ccc(CNC(=O)[C@]([O-])([SiH3])c3cccc(C)c3)cc2)cc1) `ZINC001264587634.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264587634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264587634/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001264587634 none Cc1ccc(OCCCC(=O)Nc2ccc(CNC(=O)[C@]([O-])([SiH3])c3cccc(C)c3)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 29, 29, 29, 29, 17, 17, 17, 13, 10, 13, 13, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 13, 13, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 17, 13, 13, 6, 6, 1, 2, 2, 2, 2, 2, 2, 2, 13, 13, 29, 29] 50 rigid atoms, others: [49, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264587634 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264587634 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264587634/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264587634/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264587634 Building ZINC001264640850 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264640850' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264640850 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264640850 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264640850/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264640850 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 982) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/982 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/982' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOc1ccc(Oc2ncccc2CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1) `ZINC001264640850.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264640850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264640850/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001264640850 none CCCOc1ccc(Oc2ncccc2CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 15, 15, 15, 9, 7, 7, 7, 7, 7, 7, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 15, 15, 29, 29, 29, 29, 29, 29, 29, 15, 15, 7, 7, 7, 5, 5, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 15, 15] 50 rigid atoms, others: [46, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264640850 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264640850/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264640850 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 983) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/983 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/983' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOc1ccc(Oc2ncccc2CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1) `ZINC001264640850.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264640850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264640850/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001264640850 none CCCOc1ccc(Oc2ncccc2CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 14, 14, 9, 7, 7, 7, 7, 7, 7, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 14, 14, 27, 27, 27, 27, 27, 27, 27, 14, 14, 7, 7, 7, 5, 5, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 14, 14] 50 rigid atoms, others: [46, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264640850 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264640850 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264640850/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264640850/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264640850 Building ZINC001264640850 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264640850' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264640850 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264640850 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264640850/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264640850 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 982) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/982: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOc1ccc(Oc2ncccc2CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1) `ZINC001264640850.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264640850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264640850/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001264640850 none CCCOc1ccc(Oc2ncccc2CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 15, 15, 15, 9, 7, 7, 7, 7, 7, 7, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 15, 15, 29, 29, 29, 29, 29, 29, 29, 15, 15, 7, 7, 7, 5, 5, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 15, 15] 50 rigid atoms, others: [46, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264640850 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264640850/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264640850 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 983) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/983: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOc1ccc(Oc2ncccc2CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1) `ZINC001264640850.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264640850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264640850/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001264640850 none CCCOc1ccc(Oc2ncccc2CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 14, 14, 9, 7, 7, 7, 7, 7, 7, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 14, 14, 27, 27, 27, 27, 27, 27, 27, 14, 14, 7, 7, 7, 5, 5, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 14, 14] 50 rigid atoms, others: [46, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264640850 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264640850 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264640850/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264640850/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264640850 Building ZINC001264644033 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264644033' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264644033 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264644033 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264644033/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264644033 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 984) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/984 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/984' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)ccc1F) `ZINC001264644033.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264644033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264644033/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001264644033 none CC(C)(C)OC(=O)Nc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 41, 36, 30, 36, 10, 10, 10, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 10, 10, 10, 10, 41, 41, 41, 41, 41, 41, 41, 41, 41, 30, 10, 2, 5, 5, 10, 10] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264644033 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264644033/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264644033 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 985) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/985 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/985' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)ccc1F) `ZINC001264644033.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264644033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264644033/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001264644033 none CC(C)(C)OC(=O)Nc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 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] 0 hydrogens 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, 38, 30, 38, 10, 10, 10, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 10, 10, 10, 10, 42, 42, 42, 42, 42, 42, 42, 42, 42, 30, 10, 2, 5, 5, 10, 10] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264644033 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264644033 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264644033/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264644033/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264644033 Building ZINC001264644033 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264644033' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264644033 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264644033 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264644033/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264644033 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 984) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/984: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)ccc1F) `ZINC001264644033.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264644033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264644033/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001264644033 none CC(C)(C)OC(=O)Nc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 41, 36, 30, 36, 10, 10, 10, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 10, 10, 10, 10, 41, 41, 41, 41, 41, 41, 41, 41, 41, 30, 10, 2, 5, 5, 10, 10] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264644033 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264644033/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264644033 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 985) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/985: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)ccc1F) `ZINC001264644033.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264644033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264644033/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001264644033 none CC(C)(C)OC(=O)Nc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 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] 0 hydrogens 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, 38, 30, 38, 10, 10, 10, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 10, 10, 10, 10, 42, 42, 42, 42, 42, 42, 42, 42, 42, 30, 10, 2, 5, 5, 10, 10] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264644033 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264644033 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264644033/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264644033/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264644033 Building ZINC001264770604 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264770604' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264770604 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264770604 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264770604/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264770604 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 986) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/986 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/986' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1)C1CCCCC1) `ZINC001264770604.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264770604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264770604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001264770604 none CN(C(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 24, 8, 24, 5, 10, 10, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 10, 10, 35, 37, 37, 37, 37, 37, 35, 35, 35, 10, 10, 2, 7, 7, 10, 10, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264770604 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264770604/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264770604 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 987) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/987 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/987' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1)C1CCCCC1) `ZINC001264770604.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264770604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264770604/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001264770604 none CN(C(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 25, 10, 25, 8, 10, 10, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 10, 10, 35, 37, 37, 37, 37, 37, 35, 35, 35, 10, 10, 2, 7, 7, 10, 10, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264770604 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264770604 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264770604/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264770604/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264770604 Building ZINC001264770604 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264770604' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264770604 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264770604 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264770604/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264770604 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 986) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/986: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1)C1CCCCC1) `ZINC001264770604.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264770604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264770604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001264770604 none CN(C(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 24, 8, 24, 5, 10, 10, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 10, 10, 35, 37, 37, 37, 37, 37, 35, 35, 35, 10, 10, 2, 7, 7, 10, 10, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264770604 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264770604/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264770604 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 987) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/987: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1)C1CCCCC1) `ZINC001264770604.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264770604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264770604/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001264770604 none CN(C(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 25, 10, 25, 8, 10, 10, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 10, 10, 35, 37, 37, 37, 37, 37, 35, 35, 35, 10, 10, 2, 7, 7, 10, 10, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264770604 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264770604 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264770604/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264770604/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264770604 Building ZINC001264789734 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001264789734 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 988) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/988 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/988' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@](Cc4ccccc4)CC3)c(Cl)c2)cc1) `ZINC001264789734.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264789734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001264789734 none Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@](Cc4ccccc4)CC3)c(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 16, 1, 1, 1, 7, 7, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 12, 12, 12, 14, 38, 38, 38, 38, 50, 50, 50, 50, 50, 50, 38, 34, 12, 12, 12, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 38, 38, 38, 38, 50, 50, 50, 50, 50, 50, 50, 38, 38, 38, 38, 12, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 989) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/989 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/989' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@](Cc4ccccc4)CC3)c(Cl)c2)cc1) `ZINC001264789734.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264789734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001264789734 none Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@](Cc4ccccc4)CC3)c(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 16, 1, 1, 1, 7, 7, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 12, 12, 8, 13, 35, 35, 35, 35, 50, 50, 50, 50, 50, 50, 35, 33, 12, 12, 12, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 35, 35, 35, 35, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 35, 12, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 990) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/990 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/990' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@@](Cc4ccccc4)CC3)c(Cl)c2)cc1) `ZINC001264789734.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001264789734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001264789734 none Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@@](Cc4ccccc4)CC3)c(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 16, 1, 1, 1, 7, 7, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 12, 12, 8, 14, 36, 36, 36, 36, 50, 50, 50, 50, 50, 50, 36, 32, 12, 12, 12, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 36, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 12, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 991) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/991 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/991' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@@](Cc4ccccc4)CC3)c(Cl)c2)cc1) `ZINC001264789734.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001264789734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001264789734 none Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@@](Cc4ccccc4)CC3)c(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 16, 1, 1, 1, 7, 7, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 11, 11, 8, 12, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 32, 31, 11, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 11, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264789734 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734 Building ZINC001264789734 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001264789734 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 988) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/988: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@](Cc4ccccc4)CC3)c(Cl)c2)cc1) `ZINC001264789734.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264789734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001264789734 none Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@](Cc4ccccc4)CC3)c(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 16, 1, 1, 1, 7, 7, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 12, 12, 12, 14, 38, 38, 38, 38, 50, 50, 50, 50, 50, 50, 38, 34, 12, 12, 12, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 38, 38, 38, 38, 50, 50, 50, 50, 50, 50, 50, 38, 38, 38, 38, 12, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 989) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/989: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@](Cc4ccccc4)CC3)c(Cl)c2)cc1) `ZINC001264789734.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264789734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001264789734 none Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@](Cc4ccccc4)CC3)c(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 16, 1, 1, 1, 7, 7, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 12, 12, 8, 13, 35, 35, 35, 35, 50, 50, 50, 50, 50, 50, 35, 33, 12, 12, 12, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 35, 35, 35, 35, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 35, 12, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 990) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/990: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@@](Cc4ccccc4)CC3)c(Cl)c2)cc1) `ZINC001264789734.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001264789734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001264789734 none Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@@](Cc4ccccc4)CC3)c(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 16, 1, 1, 1, 7, 7, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 12, 12, 8, 14, 36, 36, 36, 36, 50, 50, 50, 50, 50, 50, 36, 32, 12, 12, 12, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 36, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 12, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 991) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/991: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@@](Cc4ccccc4)CC3)c(Cl)c2)cc1) `ZINC001264789734.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001264789734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001264789734 none Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@@](Cc4ccccc4)CC3)c(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 16, 1, 1, 1, 7, 7, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 11, 11, 8, 12, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 32, 31, 11, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 11, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264789734 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734 Building ZINC001264789734 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001264789734 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 988) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/988: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@](Cc4ccccc4)CC3)c(Cl)c2)cc1) `ZINC001264789734.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264789734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001264789734 none Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@](Cc4ccccc4)CC3)c(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 16, 1, 1, 1, 7, 7, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 12, 12, 12, 14, 38, 38, 38, 38, 50, 50, 50, 50, 50, 50, 38, 34, 12, 12, 12, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 38, 38, 38, 38, 50, 50, 50, 50, 50, 50, 50, 38, 38, 38, 38, 12, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 989) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/989: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@](Cc4ccccc4)CC3)c(Cl)c2)cc1) `ZINC001264789734.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264789734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001264789734 none Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@](Cc4ccccc4)CC3)c(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 16, 1, 1, 1, 7, 7, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 12, 12, 8, 13, 35, 35, 35, 35, 50, 50, 50, 50, 50, 50, 35, 33, 12, 12, 12, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 35, 35, 35, 35, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 35, 12, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 990) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/990: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@@](Cc4ccccc4)CC3)c(Cl)c2)cc1) `ZINC001264789734.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001264789734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001264789734 none Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@@](Cc4ccccc4)CC3)c(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 16, 1, 1, 1, 7, 7, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 12, 12, 8, 14, 36, 36, 36, 36, 50, 50, 50, 50, 50, 50, 36, 32, 12, 12, 12, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 36, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 12, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 991) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/991: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@@](Cc4ccccc4)CC3)c(Cl)c2)cc1) `ZINC001264789734.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001264789734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001264789734 none Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@@](Cc4ccccc4)CC3)c(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 16, 1, 1, 1, 7, 7, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 11, 11, 8, 12, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 32, 31, 11, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 11, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264789734 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734 Building ZINC001264789734 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001264789734 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 988) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/988: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@](Cc4ccccc4)CC3)c(Cl)c2)cc1) `ZINC001264789734.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264789734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001264789734 none Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@](Cc4ccccc4)CC3)c(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 16, 1, 1, 1, 7, 7, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 12, 12, 12, 14, 38, 38, 38, 38, 50, 50, 50, 50, 50, 50, 38, 34, 12, 12, 12, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 38, 38, 38, 38, 50, 50, 50, 50, 50, 50, 50, 38, 38, 38, 38, 12, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 989) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/989: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@](Cc4ccccc4)CC3)c(Cl)c2)cc1) `ZINC001264789734.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264789734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001264789734 none Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@](Cc4ccccc4)CC3)c(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 16, 1, 1, 1, 7, 7, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 12, 12, 8, 13, 35, 35, 35, 35, 50, 50, 50, 50, 50, 50, 35, 33, 12, 12, 12, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 35, 35, 35, 35, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 35, 12, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 990) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/990: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@@](Cc4ccccc4)CC3)c(Cl)c2)cc1) `ZINC001264789734.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001264789734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001264789734 none Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@@](Cc4ccccc4)CC3)c(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 16, 1, 1, 1, 7, 7, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 12, 12, 8, 14, 36, 36, 36, 36, 50, 50, 50, 50, 50, 50, 36, 32, 12, 12, 12, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 36, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 12, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 991) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/991: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@@](Cc4ccccc4)CC3)c(Cl)c2)cc1) `ZINC001264789734.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001264789734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001264789734 none Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@@](Cc4ccccc4)CC3)c(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 16, 1, 1, 1, 7, 7, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 11, 11, 8, 12, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 32, 31, 11, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 11, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264789734 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789734 Building ZINC001264789960 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001264789960 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 992) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/992 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/992' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@](Cc4ccccc4)CC3)c(Cl)c2)c1) `ZINC001264789960.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264789960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001264789960 none Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@](Cc4ccccc4)CC3)c(Cl)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 17, 17, 17, 17, 27, 27, 27, 27, 27, 27, 17, 17, 8, 8, 8, 4, 4, 4, 4, 2, 4, 4, 2, 8, 8, 17, 17, 17, 17, 27, 27, 27, 27, 27, 27, 27, 17, 17, 17, 17, 8, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 993) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/993 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/993' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@](Cc4ccccc4)CC3)c(Cl)c2)c1) `ZINC001264789960.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264789960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001264789960 none Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@](Cc4ccccc4)CC3)c(Cl)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 16, 16, 16, 16, 27, 29, 29, 28, 29, 29, 16, 15, 8, 8, 8, 4, 4, 4, 4, 2, 4, 4, 2, 8, 8, 16, 16, 16, 16, 27, 27, 29, 29, 29, 29, 29, 16, 16, 16, 16, 8, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 994) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/994 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/994' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@@](Cc4ccccc4)CC3)c(Cl)c2)c1) `ZINC001264789960.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001264789960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001264789960 none Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@@](Cc4ccccc4)CC3)c(Cl)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 17, 17, 17, 17, 26, 26, 26, 26, 26, 26, 17, 17, 8, 8, 8, 4, 4, 4, 4, 2, 4, 4, 2, 8, 8, 17, 17, 17, 17, 26, 26, 26, 26, 26, 26, 26, 17, 17, 17, 17, 8, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 995) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/995 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/995' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@@](Cc4ccccc4)CC3)c(Cl)c2)c1) `ZINC001264789960.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001264789960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001264789960 none Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@@](Cc4ccccc4)CC3)c(Cl)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 14, 14, 14, 14, 25, 26, 26, 26, 26, 26, 14, 13, 8, 8, 8, 4, 4, 4, 4, 2, 4, 4, 2, 8, 8, 14, 14, 14, 14, 25, 25, 26, 26, 26, 26, 26, 14, 14, 14, 14, 8, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264789960 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960 Building ZINC001264789960 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001264789960 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 992) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/992: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@](Cc4ccccc4)CC3)c(Cl)c2)c1) `ZINC001264789960.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264789960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001264789960 none Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@](Cc4ccccc4)CC3)c(Cl)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 17, 17, 17, 17, 27, 27, 27, 27, 27, 27, 17, 17, 8, 8, 8, 4, 4, 4, 4, 2, 4, 4, 2, 8, 8, 17, 17, 17, 17, 27, 27, 27, 27, 27, 27, 27, 17, 17, 17, 17, 8, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 993) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/993: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@](Cc4ccccc4)CC3)c(Cl)c2)c1) `ZINC001264789960.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264789960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001264789960 none Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@](Cc4ccccc4)CC3)c(Cl)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 16, 16, 16, 16, 27, 29, 29, 28, 29, 29, 16, 15, 8, 8, 8, 4, 4, 4, 4, 2, 4, 4, 2, 8, 8, 16, 16, 16, 16, 27, 27, 29, 29, 29, 29, 29, 16, 16, 16, 16, 8, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 994) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/994: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@@](Cc4ccccc4)CC3)c(Cl)c2)c1) `ZINC001264789960.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001264789960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001264789960 none Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@@](Cc4ccccc4)CC3)c(Cl)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 17, 17, 17, 17, 26, 26, 26, 26, 26, 26, 17, 17, 8, 8, 8, 4, 4, 4, 4, 2, 4, 4, 2, 8, 8, 17, 17, 17, 17, 26, 26, 26, 26, 26, 26, 26, 17, 17, 17, 17, 8, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 995) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/995: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@@](Cc4ccccc4)CC3)c(Cl)c2)c1) `ZINC001264789960.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001264789960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001264789960 none Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@@](Cc4ccccc4)CC3)c(Cl)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 14, 14, 14, 14, 25, 26, 26, 26, 26, 26, 14, 13, 8, 8, 8, 4, 4, 4, 4, 2, 4, 4, 2, 8, 8, 14, 14, 14, 14, 25, 25, 26, 26, 26, 26, 26, 14, 14, 14, 14, 8, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264789960 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960 Building ZINC001264789960 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001264789960 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 992) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/992: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@](Cc4ccccc4)CC3)c(Cl)c2)c1) `ZINC001264789960.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264789960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001264789960 none Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@](Cc4ccccc4)CC3)c(Cl)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 17, 17, 17, 17, 27, 27, 27, 27, 27, 27, 17, 17, 8, 8, 8, 4, 4, 4, 4, 2, 4, 4, 2, 8, 8, 17, 17, 17, 17, 27, 27, 27, 27, 27, 27, 27, 17, 17, 17, 17, 8, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 993) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/993: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@](Cc4ccccc4)CC3)c(Cl)c2)c1) `ZINC001264789960.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264789960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001264789960 none Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@](Cc4ccccc4)CC3)c(Cl)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 16, 16, 16, 16, 27, 29, 29, 28, 29, 29, 16, 15, 8, 8, 8, 4, 4, 4, 4, 2, 4, 4, 2, 8, 8, 16, 16, 16, 16, 27, 27, 29, 29, 29, 29, 29, 16, 16, 16, 16, 8, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 994) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/994: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@@](Cc4ccccc4)CC3)c(Cl)c2)c1) `ZINC001264789960.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001264789960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001264789960 none Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@@](Cc4ccccc4)CC3)c(Cl)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 17, 17, 17, 17, 26, 26, 26, 26, 26, 26, 17, 17, 8, 8, 8, 4, 4, 4, 4, 2, 4, 4, 2, 8, 8, 17, 17, 17, 17, 26, 26, 26, 26, 26, 26, 26, 17, 17, 17, 17, 8, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 995) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/995: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@@](Cc4ccccc4)CC3)c(Cl)c2)c1) `ZINC001264789960.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001264789960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001264789960 none Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@@](Cc4ccccc4)CC3)c(Cl)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 14, 14, 14, 14, 25, 26, 26, 26, 26, 26, 14, 13, 8, 8, 8, 4, 4, 4, 4, 2, 4, 4, 2, 8, 8, 14, 14, 14, 14, 25, 25, 26, 26, 26, 26, 26, 14, 14, 14, 14, 8, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264789960 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960 Building ZINC001264789960 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001264789960 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 992) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/992: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@](Cc4ccccc4)CC3)c(Cl)c2)c1) `ZINC001264789960.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264789960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001264789960 none Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@](Cc4ccccc4)CC3)c(Cl)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 17, 17, 17, 17, 27, 27, 27, 27, 27, 27, 17, 17, 8, 8, 8, 4, 4, 4, 4, 2, 4, 4, 2, 8, 8, 17, 17, 17, 17, 27, 27, 27, 27, 27, 27, 27, 17, 17, 17, 17, 8, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 993) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/993: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@](Cc4ccccc4)CC3)c(Cl)c2)c1) `ZINC001264789960.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264789960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001264789960 none Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@](Cc4ccccc4)CC3)c(Cl)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 16, 16, 16, 16, 27, 29, 29, 28, 29, 29, 16, 15, 8, 8, 8, 4, 4, 4, 4, 2, 4, 4, 2, 8, 8, 16, 16, 16, 16, 27, 27, 29, 29, 29, 29, 29, 16, 16, 16, 16, 8, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `2' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960/2 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 2 (index: 994) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/994: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@@](Cc4ccccc4)CC3)c(Cl)c2)c1) `ZINC001264789960.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001264789960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001264789960 none Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@@](Cc4ccccc4)CC3)c(Cl)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 17, 17, 17, 17, 26, 26, 26, 26, 26, 26, 17, 17, 8, 8, 8, 4, 4, 4, 4, 2, 4, 4, 2, 8, 8, 17, 17, 17, 17, 26, 26, 26, 26, 26, 26, 26, 17, 17, 17, 17, 8, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `3' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960/3 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 3 (index: 995) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/995: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@@](Cc4ccccc4)CC3)c(Cl)c2)c1) `ZINC001264789960.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001264789960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001264789960 none Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2ccc([N@]3CC[N@@](Cc4ccccc4)CC3)c(Cl)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 14, 14, 14, 14, 25, 26, 26, 26, 26, 26, 14, 13, 8, 8, 8, 4, 4, 4, 4, 2, 4, 4, 2, 8, 8, 14, 14, 14, 14, 25, 25, 26, 26, 26, 26, 26, 14, 14, 14, 14, 8, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264789960 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 2: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960/2.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960/0.* 3: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960/3.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264789960 Building ZINC001264793355 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264793355' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264793355 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264793355 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264793355/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264793355 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 996) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/996 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/996' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC1(c2ccc(F)cc2)CCCCC1) `ZINC001264793355.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264793355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264793355/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001264793355 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC1(c2ccc(F)cc2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 3, 3, 3, 22, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 3, 13, 13, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 135 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264793355 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264793355/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264793355 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 997) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/997 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/997' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC1(c2ccc(F)cc2)CCCCC1) `ZINC001264793355.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264793355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264793355/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001264793355 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC1(c2ccc(F)cc2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 5, 7, 7, 3, 3, 1, 1, 1, 1, 2, 2, 2, 19, 42, 43, 43, 42, 43, 43, 43, 42, 42, 42, 42, 42, 3, 3, 3, 7, 7, 6, 7, 7, 3, 3, 3, 2, 11, 11, 43, 43, 43, 43, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 135 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264793355 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264793355 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264793355/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264793355/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264793355 Building ZINC001264793355 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264793355' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264793355 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264793355 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264793355/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264793355 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 996) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/996: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC1(c2ccc(F)cc2)CCCCC1) `ZINC001264793355.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264793355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264793355/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001264793355 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC1(c2ccc(F)cc2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 3, 3, 3, 22, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 3, 13, 13, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 135 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264793355 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264793355/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264793355 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 997) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/997: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC1(c2ccc(F)cc2)CCCCC1) `ZINC001264793355.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264793355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264793355/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001264793355 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC1(c2ccc(F)cc2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 5, 7, 7, 3, 3, 1, 1, 1, 1, 2, 2, 2, 19, 42, 43, 43, 42, 43, 43, 43, 42, 42, 42, 42, 42, 3, 3, 3, 7, 7, 6, 7, 7, 3, 3, 3, 2, 11, 11, 43, 43, 43, 43, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 135 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264793355 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264793355 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264793355/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264793355/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264793355 Building ZINC001264795444 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264795444' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264795444 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264795444 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264795444/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264795444 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 998) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/998 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/998' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(Br)c(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1OC) `ZINC001264795444.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264795444.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264795444/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001264795444 none COc1cc(Br)c(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 15, 15, 15, 15, 15, 5, 5, 1, 5, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 15, 15, 15, 30, 30, 30, 30, 15, 5, 5, 1, 5, 15, 30, 30, 30] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264795444 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264795444/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264795444 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 999) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/999 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/999' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(Br)c(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1OC) `ZINC001264795444.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264795444.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264795444/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001264795444 none COc1cc(Br)c(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 14, 14, 14, 14, 14, 5, 5, 1, 5, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 14, 14, 14, 29, 29, 29, 29, 14, 5, 5, 1, 5, 14, 29, 29, 29] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264795444 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264795444 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264795444/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264795444/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264795444 Building ZINC001264795444 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264795444' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264795444 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001264795444 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264795444/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264795444 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 998) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/998: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(Br)c(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1OC) `ZINC001264795444.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264795444.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264795444/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001264795444 none COc1cc(Br)c(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 15, 15, 15, 15, 15, 5, 5, 1, 5, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 15, 15, 15, 30, 30, 30, 30, 15, 5, 5, 1, 5, 15, 30, 30, 30] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264795444 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 mkdir: created directory `1' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264795444/1 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264795444 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 1 (index: 999) grep: /scratch/xiaobo/129831/xbf-8058088.32/working/3D/999: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(Br)c(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1OC) `ZINC001264795444.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001264795444.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264795444/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001264795444 none COc1cc(Br)c(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 14, 14, 14, 14, 14, 5, 5, 1, 5, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 14, 14, 14, 29, 29, 29, 29, 14, 5, 5, 1, 5, 14, 29, 29, 29] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264795444 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264795444 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264795444/0.* 1: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264795444/1.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264795444 Building ZINC001264829197 mkdir: created directory `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264829197' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264829197 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for ZINC001264829197 mkdir: created directory `0' /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264829197/0 /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264829197 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Protomer 0 (index: 1000) Found valid previously generated 3D confromation in /scratch/xiaobo/129831/xbf-8058088.32/working/3D/1000 `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/1000' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2nc3c(s2)C[C@@H](c2ccccc2)CC3)cc1Cl) `ZINC001264829197.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001264829197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264829197/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001264829197 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2nc3c(s2)C[C@@H](c2ccccc2)CC3)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 14, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 16, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 4, 6, 11, 11, 6, 11, 11, 11, 11, 14, 14, 11, 14, 14, 11, 11, 6, 6, 6, 14, 14, 14, 6, 6, 4, 11, 11, 14, 14, 12, 14, 14, 11, 11, 11, 11, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 78 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264829197 /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Finished preparing ZINC001264829197 Recording results /scratch/xiaobo/129831/xbf-8058088.32/working /scratch/xiaobo/129831/xbf-8058088.32 Appending to /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.* 0: /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264829197/0.* Removing working files in /scratch/xiaobo/129831/xbf-8058088.32/working/building/ZINC001264829197 /scratch/xiaobo/129831/xbf-8058088.32 Compressing combined databse files /scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.db2.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/xiaobo/129831/xbf-8058088.32/finished) ======================================================= Finalizing... removed `/scratch/xiaobo/129831/xbf-8058088.32/working/3D/1001' removed directory: `/scratch/xiaobo/129831/xbf-8058088.32/working/3D' rmdir: removing directory, `/scratch/xiaobo/129831/xbf-8058088.32/working/building' rmdir: removing directory, `/scratch/xiaobo/129831/xbf-8058088.32/working' /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/logs `/scratch/xiaobo/129831/xbf-8058088.32' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbf' `/scratch/xiaobo/129831/xbf-8058088.32/finished' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbf/finished' `/scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.db2.gz' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbf/finished/xbf.db2.gz' removed `/scratch/xiaobo/129831/xbf-8058088.32/finished/xbf.db2.gz' removed directory: `/scratch/xiaobo/129831/xbf-8058088.32/finished' removed directory: `/scratch/xiaobo/129831/xbf-8058088.32'